For this, I will start way early on, long before the Mushroom Kingdom was formed.
Long ago, there was a magical human country constantly under the threat of collapse from territorial disputes from various dragon tribes across the land. These humans lived in a country where the royals possessed immense holy magical powers.
For many years, the too proud dragon tribes refused to join up against the humans, while the humans' magical defenses continued to keep them at bay since the time of their settlement. A constant stalemate... until an individual was born that tipped the scales.
Though the dragon tribes were too proud to team up with one another, there was a tribe of 'lesser' dragons of which all dragons subjugated as their slaves. A race of 'turtle-dragons' whom were known as the Koopa.
The dragons treated the Koopa as slaves for as long as their kind could remember. The Koopa specialized in using industrial level creative creations to upgrade the dragons, both with armor, cannons, and the like. And not only that, the powerful dragons often used their powerful but chaotic magics to fuel their dragon powers... and they often were willing to sacrifice the lives of their Koopa slaves, due to their rapid reproduction cycles, as sacrificial channels for that magic, often using them as sacrificial kamikaze projectiles or magic shields.
This servitude encompassed the Koopa way of life. Till one day, a rather... unusually prideful Koopa became born. To be precise, Bowser's unnamed father.
Bowser's father, for now, shall just be known as Powser(pa bowser) till a better name is figured out.
One day, the rather prideful koopa mechanic Powser was working for the dragons, annoyed with having to obey the ol' blowhards as usual, when he had the 'fortune' of being on the front lines against the humans as punishment for his uppity mouth. Many thought he was lucky to come out of it alive, since another dragon tribe also attacked both the humans and their forces at the same time. But during that fight, he learned many things that changed his viewpoints on the world.
First off, due to the other rival tribe, Powser learned that it wasn't just his Koopas that were suffering the rule of the dragons, but others as well had to serve different types of dragon tribes out there.
The second thing Powser noticed was the unique and powerful ways the enemies wielded magic as compared to the more chaotic wasteful methods the prideful dragons used. It was awe-inspiring, making him realize there truly were beings able to stand up to their cruel overlords.
With these in mind, he realized that his 'mighty masters' weren't as all powerful as they made themselves out to be. They're just as mortal as any of the rest of them. The superstitious stories they told their kind were utter nonsense meant to prevent them from realizing they were just mere mortals. They can die... and the Koopa don't HAVE to listen to them.
Of course, though they don't HAVE to listen to them, Powser knows he wouldn't survive turning against them on his own. He's not stupid. His best chance is to increase his powers. Koopa, even with their technical excellence, always had a talent for absorbing and casting magic to enhance their overlords' abilities. But, it's so reckless how they do it that doing so themselves is potentially be suicidal. They need something less likely to explode in their faces. They need the magic of the humans. But how?
He'd need to get into contact with them somehow. But, with how well known he is as a mechanic, there's no way he could escape without being noticed. He'll need another way to contact them. A messenger of some sort that the dragons will overlook.
At that, he suddenly remembers something. A while back, he saved a rather unusual creature that was always hiding in the shadows. He was curious about it and set a trap, only to befriend it. It was a strange sub-species of dragon. Flatter face, human like hands.... and strangely, lacking scales, having lots of ugly boils scattered asymmetrically across its skin. In other words, something very hideous. But, were it not for his trap, he would have never spotted it due to its stealthy movements.
After he had trapped it, he strangely befriended the entity and set it free.
Now, since he set it free, perhaps it can help him gain his own freedom. Such stealth should allow it to get in and out of the territory with ease.
Eventually, Powser finds him, but his friend is refraining from helping. He's scared of what others would think about his grotesque appearance. Powser agrees. With a look like that, the humans would likely attack first, and ask questions later. But then, he comes up with an idea.
The next day, he brings to the creature a new outfit to hide himself in. After putting it on, Powser says: "Say hello to the new you. I call it... 'Shy Guy'!" I doubt I need say that his friend and his species quickly joined the fad after that, since it let them speak to others without worrying about their appearance.
After granting his new Shy Guy friend this disguise, he readily accepts the mission from Powser to contact the humans for help.
After contacting them, the humans are reluctant to accept at first till Powser can give something in return. Considering the humans specialize in magic and the koopa in tech, it's an easy deal to make for him. Tech from him and the allies he can gain in return for magic training and aid against his Overlords.
After beginning his training, Powser slowly tries to gain further allies among his kind, till eventually, the day comes to overthrow the overlords, the dragons ruling that section of the kingdom in a united assault, the Koopa and Humans working together.
From there, it quickly became a war against the dragons, along with a long campaign of uniting the enslaved Koopa to Powsers rule.
Along the way, Powser becomes great friends with the current prince of the kingdom, enough to fight alongside him many a time. Enough to... see a rather recurring event come to pass. That being a novice sorceress constantly pestering him about them being destined to be together. That she'll never let anything come between them.
Later, even on his death bed, Powser can never forgive himself for passing her off as harmless back then.
This novice sorceress was obsessed with the prince. And after one failure, trying to figure out how to MAKE him hers, she happens upon an unusual source of inspiration.
As luck would have it, she found such.
She was looking through a magically enhanced telescope among the stars when she found an unusual war going on in space.... the Shroobs taking over their home planet. More precisely, she saw them converting their fallen foes into more loyal Shroobs to join their ranks. A parasitic sapient mushroom.
With that in mind, she started to study mushrooms and how to combine them with her magic, experimenting to extremes in her obsession to have the prince, as well as have her revenge upon Powser for his meddling.
Once she became good enough to combine her magics with mushrooms, she tried to experiment with a method to make a permanent end to the dragons by infesting and changing them from the inside.
She somewhat succeeded, inadvertently creating the Yoshis. However, by the time she finished that tribe of dragons, she left their island only to discover the remaining dragon tribes had already been decimated through the combined teamwork of the humans and koopas, whose alliance she had underestimated.
Frustrated, during the peace, she tried to convince him by showing her new might... only to have him be horrified and sending soldiers to apprehend the terrible witch for her evil magics.
Unfortunately, losing her hope of doing so nicely from this causes her to decide to force her goals, and gain his love, whether he likes it or not.
With that in mind, she tries to infest humans with her mushrooms when the nice approach fails to allow her near enough to even speak to the source of her obsession. Unfortunately, doing so had unexpected consequences, mixing with their magical potential and turning them into monsters. But surprisingly, this very instability also made their forms, and minds, easier for her to shift to her will.
With this done, she tries to get some more... test samples... while trying to keep unnoticed. She then experiments upon her kidnapped victims. Eventually, she learns to control them, turning them into shapeshifting human/mushroom hybrid monsters, while also disguising them as an unassumingly cute form. A form that she calls a Toad.
She starts using them in small groups to try and take over cities, but as dangerous as they are, they just aren't strong enough to do well against the trained magic soldiers, or even occasional well equipped Koopa, that show up. So, she backs off her attacks and tries to rethink her strategies.
As she goes over her notes, she realizes one of the reasons why mushrooms are so hard to get rid of is their high rate of reproduction. Her lone Mushroom monsters can reproduce a ton, though they lack the magical fortitude of her hybrids.
As for her hybrids though, they're more human than mushroom. They can't reproduce as fast as long as they remain too human. They need to be converted further. It's not long till she creates her first elite forces, by putting her experiments into coccoons to convert them more fully into a mushroom organism that maintains its humanoid characteristics and magical potential powers. Only now... they can fairly rapidly reproduce, even while battle. They even have more advanced capacity for shapeshifting, allowing them to shrink, grow, and more even more easily than her original mushroom creations, thanks to their magical potential empowering their abilities ever further.
The fact that they have magical powers on top of that makes them extremely deadly.
With these forces under her control, she starts to create a very formidable force, wiping out more and more of the human soldiers that try to stop her. It gets to the point where the humans start calling in the aid of the Koopas, which pushes her into a stalemate position. Worse even, since her forces are being forced back, and eventually, back into hiding.
Frustrated and realizing that she has to consider their allies and potential allies as well, she decides to pull back and see if there are ways to further push her Toads. They originate in Mushrooms, and thus, she decides to start by re-researching it fully till she can come up with a plan.
After some time, she comes up with a two-fold plan.
First, she creates a test location for her greatest creation. An underground mushroom network, much like how normal mushrooms are hard to kill due to their underground network of connections... but she takes it a step forward. By implementing her mushroom control of giant mushroom creatures with the very land as its nutrients, she starts to take control of the land of the kingdom itself, turning it into a... Mushroom Kingdom, or at least the starting of it.
With the land itself becoming a slow, powerful force for her to control that spreads through the land itself, it doesn't take long for even her creative enemies to become overwhelmed.
Meanwhile, while her landshrooms slowly spread, she sends out her Elite Toads, disguised as harmless merchants, out to other lands outside the boundaries of the Kingdom to form 'good relations' outside of it, while also spreading slander about the evil of the humans of the Mushroom Kingdom, along with their turtle dragon allies, the Koopas. But at the same time, stating that their tyranny will soon fall thanks to their mushroom queen, and the 'merchants' are merely 'bartering for added supplies' to make finishing the war against their weakening former tyrants easier.
By painting the humans and Koopas of the land as the villains in every country outside of their land, she ensures that they don't gain allies due to them being labeled as evil.
Though it takes time, this Mushroom Queen's plans work. No one comes to their aid, and though there's difficulties, the Landshrooms eventually separate and convert all the humans in the land to their own kind. Even the mightiest of them all, the land's prince turned king(due to his father's death) gets captured by them, though his mighty holy magics make it very difficult.
It takes a mushroom trap of sorts to deal with the king, the trap regenerating faster than his immense magical powers can destroy it. On its own, the mushroom trap's attacks are negligible to the mighty king. But, it doesn't have to be stronger than him. It just needs to outlast him, and outlast him it does, till he finally exhausts himself to a vulnerable enough state to break his mind and take him over as her mightiest slave.
Despite being braindead, that's fine to the now insane queen. She wanted him for his looks and the potential power and perfectness he seemed to be. Perfect for making her children all the more powerful and wonderful, and she was obsessed enough with her being the perfect mate for her that she went to any and all lengths to do so. With him, her ascendance to being a 'Queen' is not only guaranteed, but it also guarantees all the best for her future children by combining her bloodline with a mighty bloodline like his, altered though it is from the mushroom possession. But, she thinks that's all the better, since it should strengthen the link her children would have with the mushrooms she used to take over the kingdom.
Meanwhile, the Koopas aren't doing much better than the humans. They've been scattered, forced to use underground brick stone caverns to protect themselves from the ever watchful landshrooms and their mushroom networks.
Despite the overwhelming disadvantage, the Koopa continue to fight the Toads, as best as they can manage. But in the end, it's not long till the queen's Landshrooms have infested all but the most volcanic of terrains.
And worse for Powser... in the conflict against her toads, he lost his wife, shortly after she gave birth.
And after that, just to rub salt in the wounds, he gets message that all his calls for aid outside the kingdom were refused, due to them having heard of all the 'evil' things the koopas and their allies have done, not wanting any part of them.
This finally is the breaking point for Powser. He thinks: "So, I'm the bad guy, am I? The big evil in the kingdom? ...Fine then. They want to label me as the villain? Then, I'll start acting the part! No more Mr. Nice Koopa!"
With that, he begins to take more cruel and underhanded methods to his assaults. No longer straight shows of honorable fighting power. No longer just re-adjusting the tech into koopa weapons to fight foes from within their ranks and from without. Now, he starts using every underhanded method he can think of, as long as it means gaining an advantage against the toads. Even if it means experimenting upon their deceased bodies to do so.
At one point, one of his koopa mages discovers something on accident. By targetting a tendril of a cut-off Landshroom with a spell, it can effect a large part of the mushroom network. Through refining this process, they develop a way to use the killed Landshrooms as transformed... transport pipes, using the newly green pipe structures to transfer their forces directly into and out of enemy territories.
With the guerilla tactics this allows the koopas to start, they start to use brick structures, hardened from refineries in volcanic locations, to create strongholds throughout the land, the brick structures being unable to be infected by the landshrooms due to their solid structures.
Not only this, but on the way, Powser is able to gain the allegiance of various species. Like Boos, Spinies, and various others.
He even encounters the Goombas, a failed experiment left to slave around in the queen's oldest magic laboratory. They were designed to be purely carnivorous, meant to be temperamental and super aggressive, but something went wrong in the process of developing these new mushroom creatures. Sure, they were short tempered, but they were surprisingly pacifists, not wanting to hurt creatures of the natural order.
When Powser saved them, brought them out of the labs, and showed them what their creator had been doing, they were enraged. Their own creator had been secretly harming many of the land's natural creatures for her pursuits. They were fine getting harmed themselves, but for the land to suffer like this? Angry, they wanted to help Powser, swearing to work with him till they died to stop her plague.
Powser would be glad for their help, but asks them to delay it. Right now, their forces have started to make a dent in their forces. But really, all of their forces are forces that lost something to the Queen. The Goombas though have never had the chance to have that yet. They've never had to fight before in their lives to survive, and therefore would likely only slow them down.
So, instead, he asks them to first leave the kingdom. Live their lives and find out ways to survive in the normal world. If they can do that, then he may call on their aid one day. And in the meantime, perhaps they can help fix the bad PR campaign the queen has run on the koopa abroad. At least in that, the Goombas can help without risking their lives. They should have a chance to find something to cherish. Only by finding something to cherish can they truly fight with all their strength, after all.
The Goombas accept these terms, though reluctantly. And they swear, for his saving them, that if he or his brethren ever need them, they need but call on them for help.
And while things were starting to go better for Powser's forces, the same could not be said for the Queen.
She finally got pregnant from her weakened king, as she always wanted. But, ever since, her powers have been somewhat unstable, and her body hasn't been doing that well either due to the pregnancy hormonal issues. And the fact that the Koopa forces have found a way to fight back isn't making things any easier on her.
Since her Toads all fight better on soil they can infect and link to the mushroom network through, they are at a notable disadvantage in the firey and brick structures they've been starting to use. She needs to find an alternative way to exterminate these Koopa pests and their allies.
At that, she gets an idea. Someone to exterminate pests... an exterminater is exactly whom she needs. When she still lived among humans, long before her experiments that gave her her powers, she needed to hire some now and then to clean her lab of rats. With how much these Koopa have been using these pipes they've made, they certainly are actin' like such.
But, these Koopa aren't just rats. They're formidable opponents. And worse, their magikoopas have been developing spells to multiply their forces, to compensate for how her own forces can multiply so much. They're not as skilled as her own Toads, but it's still frustrating.
She needs someone powerful. Someone brave, and someone brutal. So, she sends out message through the mushroom network to the Toads far out in the other kingdoms, even the kingdoms that their mushroom network are subtly starting to infect deeply in order to set up a new invasion and spread her reign. She gives the order to find such a warrior. Preferably one that they can pay. After all, after having taken control of the kingdom, they've also gained access to the royal treasury's spoils as well.
And when hearing of the cruel 'hero' that defeated a giant monkey from kidnapping a girl, she knew she found her pawn.
At first, she had her Toads shift to their more cute forms, playing the roles of victims while around this 'Jumpman'. His real name is unknown to her. Only his title, and that enough is good enough to keep a closer eye on him.
She nearly panics when, right in front of him, her toads are forced to take on their true form to protect her from an accidental roof collapsing, caused from a sudden koopa assault.
Very surprising to her, Jumpman doesn't seem perturbed to it. If anything, he finds it interesting. More surprising, he'll still help, as long as the pay is worth it.
At that, she asks him to prove himself first by dealing with their current issues alongside her soldiers. And he certainly proves himself. He even manages to force Powser himself to leave from the multi-pronged assault. And while the Landshrooms and Elite Toads handle clean-up with the enemies on the surface, Jumpman handles the forces that sneak into the pipeworks and the underground bases.
After such a display, he's quickly hired by the Queen, and he starts to systematically wipe out each of the Koopa bases. Much to Powser's horror, even his most well defended of bases are decimated while he's away, and his precious wife gets killed in the process.
Luckily, the son of his most loyal servant was able to hide away with Powser's baby boy, Bowser, despite his son's frequent protests to let him go rescue momma. Though crushed that his wife died, he's just glad his boy survived.
At this, he makes a decision. Before, all his guerilla warefare tactics were used to supplement his main attack forces. But, no. That was too light. He can't just use direct assaults against this new enforcer of the Queen's. For his son, he needs something to end this conflict NOW.
And while Powser is busy plotting the most underhanded of his plans against the Queen, the Queen herself is having quite the foreboding sense of dread.
Ever since she got pregnant, her powers have been a lot more difficult to control. A lot more... unstable.
Not only that, but ever since learning she was pregnant, her strongest bodyguard, the former king that impregnated her, no longer seems as... slow-witted, as before. A lot more protective too. Perhaps the shroom spores finally took over? But, for some reason, she feels it's not that simple.
And then there's Powser's forces. For years, her Toads and Landshrooms had their forces on the run, but till she hired Jumpman, Powser's forces have been slowly reclaiming the kingdom from her grasp.
Jumpman is also quite... questionable as well. She finds that though he's helping, he's greedy, enough of a show off to sacrifice her own troops if it means decimating the enemy forces, and despite her records stating that he's already married, he's flirted with her no small amount of times either, stating it could be their little secret. He's a disgusting man, and his brutality in the war is enough to even horrify her own monstrous creations.
Surprisingly, if she didn't know he was so honourless as to flirt with her when married, she may have actually accepted the offer. She found that he can be surprisingly... 'charming' when not destroying her enemies. How such a cruel man can be so charming, she may never figure out... and that mystery in her new lead fighter just makes her feeling of dread all the more potent. So much mystery, so much unknown. It's just unsettling.
And it is due to this that she decides it's time to crush Powser. Now. Before her feeling comes to be proven, she wants to get rid of her real threat.
Much to her astonishment, when she orders Jumpman to finish Powser, the leader of the enemy forces, no matter the cost.... her strongest bodyguard, the former king, requests to help him do so.
He says that he hasn't thought so clearly in years, and that he wants to do something for the kingdom. Reluctantly, the Queen allows him to go with Jumpman.
During the mission, the king acts oddly, but Jumpman shrugs it off. A mission's a mission to him, after all. As long as he gets paid, he could care less about the method.
But, when they finally get to Powser, the king makes his move, and sends Jumpman flying.
"Powser, my friend, I am glad to have this last chance to talk with you- What are you doing?! I thought we had settled for obeying the Queen?! Grr... Powser. Please lis- NO! I'm taking back control!"
In the end, Powser has to fight the shroom possessed king, weakening the shroom with precise strikes enough to grant the King a chance to take back control.
Once the king has control, he explains to Powser that the Queen is pregnant with his child, and he asks him to save his daughter from her influence. The Queen is truly evil for all she has done, but their child has yet to do anything evil herself. She's a blank slate. And if anything, his daughter has helped them.
Apparently, the Queen mating with him was a BAD idea. Holy and dark magics of any sorts don't mix. Her powers have been on the decline due to them being in a chaotic state while his unborn daughter is in her. And the process of giving birth is sure to leave her even weaker. More so, it seems from what magic he could sense, there's more bursts of holy magic coming from that magical conflict than dark magics, weakening the Queen further from the inside out.
He knows it doesn't leave Powser much of a window to work with, but he pleads with Powser to save his daughter from the grasp of the Toads and their Queen.
Powser reluctantly agrees, if only in honor of his old friend.
And then the moment is ruined as Jumpman returns, furious about the sucker punch that sent him flying.
The King begs Powser to flee. He was lucky to survive Jumpman last time. He needs to stay alive to finish this, or else all their efforts will have been for naught. He'll hold off Jumpman long enough for Powser to escape.
Hating having to do this, he sees his point, and tries to escape, sending as many fire blasts at Jumpman as he can while he flees. After all, even if he's agreed to flee, doesn't mean he can't do what he can to help till they're out of sight.
... the painful results were obvious. A noble king died that day. And the castle treasury suffered a painful blow from the bonus Jumpman forced to be paid in return for such a difficult battle.
Afterwards, the Toads seemed to start acting a lot more morosely. The Queen may have decided that she no longer needed the king, but his death still brought about painful memories of nostalgia of times of the past. And her connection to the Toads and Landshrooms led to that nostalgia having a negative effect on all of the Queen's forces.
This effect proved very beneficial for Powser. Made it easy to slip in some spies to keep an eye on the Queen, as well as arrange his plans to infiltrate when she finally enters labor.
Deciding to take a rather devious route, Powser decides to make a strategy that spreads his forces extremely thin, having one magikoopa per army squad... that uses an illusion to disguise themselves as Powser.
Powser knows that Jumpman will be gunning him down. There's no way he could handle both him and the Queen at once. Jumpman alone is hard enough to beat. So, he needs to lure him away from his true goal.
However, Powser also knows that if there's multiple Powsers out there performing attacks, they'll realize that they're fakes. So, he'll have a smaller squad attempting sneaking missions, and purposefully fail at sneaking, so that they think they've found the real Powser, when it's just another magikoopa in disguise.
And while Jumpman and the shrooms are distracted, he and his elite magikoopa, Kamek's mother, will sneak in. Just a matter of figuring out when to strike.
With that in mind, thanks to some connections, he gets some Boos to sneak in to the various areas of the protected castle, with the strict orders of not allowing themselves to be found out while keeping tabs on the queen. When she goes into labor, they'd contact the resident magikoopa they would have snuck in to both contact Powser and also act as a magical waypoint for Powser's elite magikoopa to teleport him and a small squad of forces to.
With those set up, the mission began. And Powser's ploy played Jumpman like a fiddle. Causing him to go from location to location, only to get frustrated as the Magikoopas keep telling him: "Your target is in another location." ...the equivalent statement of which his family later gets hounded by.
While Jumpman is distracted, Powser and his elite magikoopa sneak into the Mushroom Castle, waiting for her to finish giving birth while their plan spreads her army as thin as possible across the kingdom.
For a while, Powser and the Magikoopa wait in hiding. When the Queen is led away to recover, the newborn is left in the care of her newly promoted elite guard captain, Toadsworth. Though fairly young, he's been very promising.
They try to ambush him. They're able to deal some serious damage, but not outright stop him as intended. Having failed to take him out, the elite magikoopa sets up a sound proof shield over them as they battle.
The battle proves a bit rough. Especially when the baby Toadsworth is carrying starts to have quite the effect on him during battle till he's knocked unconscious. Whenever the baby's magic pulses, his injuries heal, but he appears to shrink under the baby's cries. As he shrinks, dark energy seems to emit from him, disbursing.
Gradually, he gets weakened enough to be knocked out in a single strike, and as she flies through the air, Powser leaps and catches her, despite his injuries.
It doesn't take long for them to bond, especially since she's the baby of Powser's recently deceased best friend. ...which makes it all the harder when he goes to finish Toadsworth and she starts crying.
In the end, though he hopes he won't regret it, he decides to have his magikoopa just bind the unconscious Toad. Wrap him up in a little bow even. For now, he'll leave the toad and baby Peach to his elite Magikoopa. He'll continue on to finish off the queen. She should be weak now, and without her two highest tiered elite guard around, he can handle the rest with just some of her buff spells. With her skills, she can place them on him and let him activate him at will, transforming mid-battle from form to form to face the queen. Considering how weak the Queen is, the buffs should last plenty long enough for him to finish her, considering their last face-to-face battle.
After he leaves his elite magikoopa behind though, reinforcements show up, forcing Kamek's mom to have her hands full with both fighting them off and keeping Peach safe and in her grasp.
Meanwhile, Powser fights his way through the Toads playing 'caretaker' with the tired Queen, easily slaughtering the high tiered Toads by freely changing his transformations for hard to predict power combos.
Irritated, the Queen comments: "...You can't even MAKE good help these days. Fine. I'll handle you myself."
The Queen proves to be a much harder opponent, but not too much for Powser, his transformations allowing him to take her down without too much difficulty.
Furious, the Queen gets desperate, saying that she has no choice. She casts a spell that knocks Powser back into the wall... as the dead Toads around her start to disentegrate, their essence being pulled into her...
"You know... it's fitting. I used the toads to take over this land. And now, I will become one to keep it!"
After a few moments, the spell completes in a flash of light, transforming the once beautiful queen into a giant mushroom monstrosity, countless mushroom segments growing together to form her monstrous form, asymmetrical in design due to the different types of elite caretaker Toads she has absorbed into her being.
As the eruptive force of her transformation completes, things get more difficult for Kamek's mom. The reinforcements just keep coming, and in the middle of it, Peach escaped her protective force field that was placed on her during the battle.
Young Peach, curious about Powser, crawls towards the room she left him leave towards.
Meanwhile, though fairing admirably, Powser's having a difficult time against the Queen. He can't even get to her main body as long as the other revived elites that have become part of her now giant form keep regenerating. He manages to harm her some, but his opening to do so is limited, even with his mighty form combo attacks. And the form buffs his elite magikoopa granted him will be running out soon.
Too soon, as it turns out. Right as he seems to stagger her main body from the amount of damage he's managed, the form buffs finally wear off right as he is going in to attack... which the queen takes full advantage of, counterattacking with a vengeance.
After the first blow however, Peach just happens to crawl in, seeing Powser thrown bodily against the wall. She starts to cry, as Powser, clumsily, tries to avoid the Queen's rampant fury.
In the Queen's blind rage, the room quickly starts to crumble. However, it doesn't take long for young Peach's cries to overcome the noise. Avoiding the falling rubble and frantic attacks, the exhausted Powser makes his way to her, saving her from the falling debris.
Needless to say, having to protect a baby while fighting the strongest enemy he's ever faced puts Powser in a serious handicap situation.
Eventually, exhausted and trying to protect Peach, Powser ends up suffering a fatal injury from some of the Queen's tendrils.
Cackling in glee, the Queen slowly stomps towards Powser.
With reluctant acceptance, Powser looks down at the baby. He appologizes that he couldn't follow her father's wishes and save her. But, at least he went down fighting.
The gentle look Powser grants her, that of a father almost, is enough to stop Peach from crying briefly. Then, she turns towards the Queen, the 'monster' who hurt her protector. With a baby like scream, she yells... and her holy magic erupts in a massive blast towards the Queen. The Queen is pushed back, screaming in pain as the holy magic surges against her. And with Peach born with a natural link to the Toads, her magic also finds access to that connection, going right down the Toadstool strange veins now cursing through the Queen's fused form, bypassing all her dark magic defenses, burning her from both within and without.
At first, Powser is gobsmacked at the baby's surprising power... before smiling as he sees and opportunity, pouring all that's left of his own mana into her's, enhancing and guiding it, making sure that it completely gets rid of her, down to the smallest of cells.
Sensing the loss of their Queen, all the Toads moan in sorrow. Enough to give Kamek's mom time to check on her boss, thinking he actually did it. ...only to become horrified when she finds the state he's in, rushing over to try and heal him.
He thanks her, but brushes off the attempts. He's got internal injuries and blood in his lungs. "The best you can do at this point is slow my death."
After a moment, Powser pauses as he looks down at the now happy Peach, smiling up at him. In hindsight, an idea comes to him as he states, "On second thought... *cough* DO slow my death." Kamek's mom: "Master...?" Powser: "Do you still have the ability to create message recordings?" Kamek's mom: "Yes. Why?" Powser: "Cause... I'd like to give one final message... for my son..."
Giving him the crystal for the spell, Kamek's mom then takes Peach to take care of out of the view of the recording after having healed him as much as she could. She figured that he'd want this recording to be private, or relatively so at least, and thus goes to the far corner of the giant ruined battleground, to let him speak his peace.
For this next bit, I'll give the overall gist of his message, excluding the various coughs and such caused by the internal bleeding of his wounds(regardless of how much Kamek's mom tried, she couldn't heal him completely due to the wounds being internal):
"Son... The Queen... Is dead. But... I won't be around the celebrate it, despite *insert Kamek's mom's name*'s best efforts. She has, however, slowed my death long enough for my final farewell to you.
You've made me proud, son, and I love you with all my heart. Every lesson, you took to heart. You're brave, ingenuitive, proud, and persistent. Heh, you remind me of me when I was young. Never lose those parts of yourself, my boy. And never stop caring for your kingdom and its allies. Stay strong, and continue to maintain their loyalties. Keep to my lessons, and they'll never betray you.*cough*"
Looking at his claw and the blood, he realizes that the quick fix is running out. He'd best wrap this up.
"Now, Bowser... I've handled the hardest part. Without the Queen to guide them, you can eventually de-weed them and reclaim our kingdom. I have faith in you, my son. Reclaim your homeland, for those lost against the Toads and your own birthright."
His vision fading, Powser looks up, hearing the giggles of Peach. Despite hardly being able to keep his eyes open, and the coughs having interrupted his speech more and more as it went on, he realizes one more thing to do, forcing his eyes open even as his body numbs.
"And my son, there's one thing you must promise me. ...Please, keep the princess from the Toads, no matter what. The princess is more important alive than I ever knew. Don't... let them... keep the... princess... For all... our... sakes..."
At the end of this, his shaking claw finally falls, the last of his strength leaving him. Hearing him, Kamek's mom reacts: "Master...? Master Powser!"
The recording cuts off as she rushes over to him, cutting out as its recording gem gets knocked over.
Unfortunately for her, when she checks on Powser, he's already dead, her magic having not been able to keep him alive long enough to finish the recording peacefully.
Heartbroken to have the second of Bowser's parents die, she swears to do her best to ensure Bowser himself won't suffer the same fate. And since Powser was so adamant about her protecting Peach, she'll just take her with her.
With that, she grabs baby Peach and teleports off with her, along with the recording gem, to make sure they're kept safe.
Unfortunately, with Kamek's mom herself weakened from all the fighting, she can't teleport far. So, she goes to their hiding hole in the castle to call out for any surviving forces to pick her and Peach up.
Meanwhile, an extremely pissed off Jumpman finally gets back from his onslaught of Powser's forces, after having learned that Powser has been confirmed to be in the castle.
Needless to say, hearing that his prey was already dead REALLY pissed him off.
Despite his own many injuries, Jumpman fumes about not having something to dish out his anger on. Hearing this, a recovered, and for some reason nicer, Elite Toadsworth says that if he wants to fight, find the princess. She's the last source of the queen's might, and they must save her. If Jumpman wants to fight, fight those that kidnapped her.
Pleased to hear that, he's more than eager to do so. But, Toadsworth then stops him, saying he can't let him go with such injuries. It'd scare the princess. Jumpman just stares at him incredulous, but Toadsworth refuses to budge on the issue, stating he'll have some of their elite healers do so.
Jumpman's at first against it, not wanting to become some Toad in the process. Annoyed, Toadsworth accepts that condition, saying they can manage that.
So, they heal Jumpman... but merging part of themselves to him long enough to find and heal his injuries from the inside. And, to Jumpman's surprise, they do more than just that. They improve him. After having detached, his body has become somewhat malleable. This feature is later shown in his kids, such as their ability to be flattened and pop right back up from that state moments later.
Beyond pleased, and eager to test his new powers, he then goes with some Toads to find the kidnappers, to test just how strong he has become.
While waiting for word on the Koopa movements, a distraught Toadsworth decides to link up to the Toads underground network to accelerate his healing. But, this has an unexpected effect.
Due to the effects of Peach's holy magic and her affinity with the Toads, she unintentionally purified Toadsworth to a degree, making him less evil at heart, and the evil magic that powered him was disbursed, shrinking him to a degree as well. And by linking to the mushroom network, the remnants of the holy energy within him also spreads into the network, having an effect on any Toad that links up to it, including the Elites preparing to accompany Jumpman to find the princess as soon as Koopa movement has been found.
And despite efforts to go unnoticed, it doesn't take long for them to locate Kamek's mom as she and her reinforcements try to retreat with the princess, considering the fact that the angered Toads have converted a large part of the land into sapient Landshrooms.
Eventually, Jumpman catches up when they're near their latest stronghold.
At the time, Kamek had rushed ahead of the army, glad to see his mother safe. And news of Jumpman's arrival comes as they're hugging it out, glad to see each other. Needless to say, the news ruins the moment.
Realizing that as long as he's being paid, Jumpman will continue to be a pain for the Koopa's. And there's no way they'd have enough money to counter offer him away. But, Jumpman's been fighting constantly. Surely, he's got to be weakened by now. So, she thinks she should be able to beat his weakened state. But... just in case... she turns to her son.
She tells him that she loves him, but she needs him to promise her something. Powser is dead, and that means only Bowser remains of his lineage. She wants Kamek to promise her that he'll not only keep Bowser and himself safe, but also help raise him to be the strong Koopa leader that their kingdom needs, just in case she's not around to do so. Should Jumpman come, he and Bowser must hide, no matter what. Hide... and get stronger. One day, Bowser may become strong enough to avenge his father, but he must live long enough to gain that strength.
Kamek readily agrees, the war having forced him to mature somewhat quickly and understanding, reluctantly, what his mother means.
Lastly, before departing, she gives Kamek the recording from Powser. She tells him to only show it to him when Kamek thinks Bowser's grown strong enough to face the Toads' armies. Otherwise, he'd just get himself killed in trying to fulfill his last wish. For now, just tell him to make sure to live, to become a strong and proud Koopa King like his father, cause if he doesn't do that, he'll never be able to fulfill his father's dying wish.
Kamek agrees. After which, his mother teleports onwards, intent to return to the battlefield against Jumpman and the Toads, to give their base enough time to evacuate in case she can't stop Jumpman.
With that, Kamek's mom leaves. When she arrives at the battlegrounds, she hears a rather peculiar report. Jumpman has come alongside the Queen's elites, but they seem... different somehow. Less aggressive, smaller, and less powerful. Though unfortunately, Jumpman has changed as well. He's performing moves he's never done before, and he's decimating their forces. Worse, it seems as if all the injuries he had incurred earlier in the reports have somehow miraculously healed.
This horrifies Kamek's mother, but she won't back down. She has the forces slow him down as much as she can, while she prepares all her best spells for the conflict ahead.
Much to her disappointment though, she's not the only one to come up with upgrades. Jumpman, feeling great after the mushroom incorporation, gets an idea as he sees some of the nearby dead Toads. In a deranged idea, he decides to take a taste of one of his dead Toad allies, and he gets temporarily empowered by it.
In the end, the cruel methods get the two at a stalemate, with Jumpman's own allies fearing him. To get a boost, he then leaps to the nearest landshroom and takes a bite out of it. Going giant in the process, he easily finishes off Kamek's mom... along with part of his own army before the power boost wears off. Though, thanks to Jumpman not killing him, the info of what he did and the results of it quickly travelled through the mushroom network.
Didn't take long for all the Toads to know that Jumpman was willing to sacrifice them just to give him a power boost. But, at the same time, it gave him the power to retrieve the princess, as he was ordered to do. And as cruel as it is, the concept behind devouring Toads to become empowered had merit to a degree, so they later on, once things had settled down, started to experiment on the production of non-sapient shrooms to eat for empowerment. Was a lot easier than expected to do, and soon, they were everywhere.
But back to the story. After Jumpman reacquires the princess, he's thrilled. Now, he's gonna get rich for this, and he's gotten more power than he ever thought possible. Due to this, he decides to take the princess back HIS way... thrill seaker style, much to the complaints of the toads. But, he just treats them as obstacles to overcome as he takes 'her highness' back to the castle. And... the princess loves the feel of the wind as he carries her on his thrillseeking, getting her to like the maniac of a mustached man.
Eventually, Jumpman gets the princess back to the Toads. They're very much relieved to have her back. But, Jumpman demands payment for all he's gone through, a lot of it after what he's been through.
The Toads are reluctant, especially after him EATING some of them for a power boost, but Toadsworth gives the okay. He even says to take as much as he can carry from the Treasury, that he deserves such after all he's gone through for them.
With their main leaders now out of the picture, the war, the Toads think, is over. Without Powser or Kamek's mom to lead, the Koopa will no longer be a threat, giving the Toads time to grieve over their newly dead Queen, as well as grant them time to focus on how to raise their new princess.
...and Jumpman makes them regret that. He finds a nearby abandoned Koopa airship, brings it over, and fills all of its chambers to bursting with treasure. He even makes giant mounds of treasure on top of the airship, to the point where he can only barely get the thing to move, intending to use it to head back to his home kingdom in the process.
Unfortunately for Jumpman, by that point, Bowser has heard of Jumpman killing Kamek's mom, and he also blames him for indirectly leading to his father's death. That combined with Kamek's anger... and that of the Koopas... well, let's just say full on assault as he leaves. They may doubt they can kill him, but Bowser's petty. He doesn't need to kill him. Just make sure that he doesn't leave the kingdom... satisfied. Basically, they put as many holes in the airship as possible, so that Jumpman's earned rewards get scattered to the winds. And the aerial assaults force Jumpman to take the scenic route out of the kingdom, flying all over the land as his stolen haul falls to the land below.
Much to Bowser's delight, by the time Jumpman escapes, one can barely see any gold through the holes of his barely flying airship. Jumpman having had too hard of a time combining both keeping the ship intact and trying to fly out of the kingdom.
From there, it was simply a matter for Bowser to just try and bring the struggling forces back together, under Kamek's guidance(and other assorted trickery) to try and bring their forces back together long enough to figure out the next plan against the Toads, planning to honor the words from his father that Kamek passed on to him.
In the meanwhile, Jumpman finally returns home as a celebrated 'hero' to his wife, Pauline. And the fact that he brought home enough gold to start a business in their town just made her all the more proud of her. That night led to the birth of Mario, named... after his father's real name, also called Mario. And the later success of the business he started with Pauline later led to his younger brother Luigi as well.
And though unknown for them at the time, the conception process passed on not only Mario Sr.'s sperm, but also some of the Toad essence he had gained as well. Inadvertantly, this helped prolong both of their youth and made their body's a tad more pliable as well, though they never realized it.
Everything seems to be going great for them. Jumpman's even gaining enough funds from the business to pay for his more esoteric hobbies. Hobbies including... capturing and tormenting of animals, like those he trained to prevent Donkey Kong Jr. from rescuing his dad while in Mario Sr.'s basement, and many darker things besides, Mario Sr. loving the feeling of superiority he gets from tormenting 'dumb animals'.
And karma strikes Mario Sr. hard when a baby Luigi happens to wander in during one of his 'animal festivals'. It traumatizes the young guy for life at all the horrible injured 'monsters' his father's acquired. His cries also attracts the attention of Pauline, whom is surprised to see the door to his private hobby room unlocked. She liked his 'bad boy' attitude and strong will, but she never could have predicted THIS horrible side of her husband.
Not long after, despite Mario Sr.'s efforts to keep the relationship going, they quickly had a falling out. ...at which point, Mario Sr. started to get more violent about keeping them around. And with his business funds, Pauline found herself trapped both physically and metaphorically via his lawyers.
Trying to figure out how to get out of the mess, she quickly realizes she's more worried about the well being of her kids instead of herself. But, how to get them to safety? It's while thinking of the babies that she thinks of the old story of storks, taking babies to be raised by their parents. And with her husband's account with animal stores... it may be possible.
Getting an idea, she discretely uses her husband's account to purchase a trained stork, and through contact with some friends that had moved to the outskirts of a 'renown Mushroom Kingdom'(thanks to the old queen's PR program), she's able to use a stork to take her babies away to be raised away from their horrible father. (leading to the Yoshi's Island games and the like.)
And thankfully for her, though unintentional, Princess Peach's very presence, with her Toadstool connections and abundance of holy magic... well thanks to her, the kingdom is starting to change into what the fake PR stories made it out to be, as the Toads and Landshrooms alike are gradually purified by her.
Eventually, the Toads are purified to the weaklings we all know them to be, having all but forgotten their shapeshifting potential, relying instead upon magic instead along with the capabilities of their 'disguise' form, which has since become their new default state. Though, it shouldn't be underestimated. Despite its small stature, it's surprisingly strong due to its compact nature.
Over time, as they take care of her, (sometime after Partners in Time)Toadsworth realizes he was trained to be a caretaker, not a father. So, eventually, they send out their toads with some of their mind control shrooms from their earlier life styles to try to find someone perfect to be a kingly father to Peach, someone without a family to miss him, and use such a shroom to re-write his memories into thinking he's her father, becoming the parent seen vaguely in some official comics.
Admittedly, that father eventually died, having taught her what was known by the Toads about magic that fit her holy powers, along with other knowledge they were able to acquire. Mostly non-combative stuff, due to the good hearted nature of their father. And he eventually died when one of the many threats Peach had to seal up reared its head.(haven't decided which, but things like the Dark Star are an example)
With all the training she received to be a ruler, along with the potential for intelligence from not one but two parents, Peach is actually overall pretty smart. However, the mixture of the chaos energies of her mom and the holy energies of her dad really caused havoc to her development when she was a baby, especially on her mind. So, despite her high intellect, that intellect comes at a slow dull witted pace, making it easy for more action prone attempts to outpace her. And the effect on her mind also made her unstable emotionally, to the point where she could change her emotions like a flip of a switch at a moments notice(case in point with her abilities in the Super Princess Peach game).
Were those problems not enough, there's also the fact that she's lived her entire life with Toads and occasional visitors. Towards visitors and what she learned from them, along with the holy energy running through her, she mostly treasures life. However, that opinion has been skewed when it comes to the Toads, whom not only regenerate at an insane rate in terms of mass production, but have also willingly sacrificed themselves eagerly and quite literally to keep her safe and happy. Literally giving their lives if it means keeping her alive and happy. ...and considering her slow-wittedness, many Toads lost their lives in her stead when having to push her out of harm's way that she didn't notice in time.
In the meantime, for the Mario bros, specifically Mario... after meeting Peach, Mario immediately becomes enamored by her, even as a baby after the events of Partners in Time. Despite that, he and his bro are eventually taken back to their foster parents at the edge of the Kingdom, whom moved in after the news the good PR of the dead Queen combined with the news of the 'war' there being over spread outside the kingdom.
Afterwards, the two bros grew up in peace, eventually becoming plumbers of a sort. A more bad ass sort: not only fixing pipes(including the magic ones formed from the corpses of old landshrooms), but also clearing out any monsters passing through them when called in as exterminators of sorts.
Also, due to his admiration of Peach at a young age, despite being too young to remember her, he grew to not only be fascinated by tales of the princess, but also strove to become worthy of her. However, that's easier said than done when he inheritted his father's natural sociopathy(he just can't understand the pain of others, helping not from empathy but due to a desire to be the best he himself can be through helping others) and his greed of the limelight. If anything, learning the truth about his dad at a later age drove him to seek to become a famous hero that far outshone his dad... to the point of it being a detriment to his younger brother Luigi, whom admired Mario for his courage and self-sacrificing nature.
Later, after Mario got famous for defeating monsters in the pipe networks, he eventually got called on to save Princess Peach via the few survivors of Bowser's curse, which turned most Toads into bricks. Mario, in desperation to save Peach, went to all lengths to save her... not caring whom he had to kill to save her, even recklessly destroying any bricks in his path, despite knowing about the curse on the Toads that turned them into them. He knew they'd sacrifice themselves to save Peach anyways, so to him, they were just unfortunate but necessary sacrifices for the greater good. Besides, if they have the chance to provide him something of use in the process, then they can at least be of use that way to help save their precious princess.
Well intentioned or not, such a thought process drove Mario, despite how twisted it was. And regardless of the sacrifices, it worked, dubbing him a hero as a result. And the rest for Mario's side of the story is history.
Then, there's Bowser's side of things.
For him, due to not being shown the message of his father as a kid, he just follows the given word from Kamek about wanting him to continue to rule the Koopa and become the best king he can be. And due to having spent time learning about his father's 'evil' methods, he did his best to become the best 'evil king' he could be, while keeping all of his dad's lessons to heart in his methods of how to do so. Those culminated in him becoming the Bowser we know of.
All the training done through his life in attempts to be worthy of his father made Bowser 'evil', but open minded. Greedy, but willing to help others in any way if it means something useful for him. He'll even selflessly help others... then say it was to prove how awsome he is. His father's goodness having not been completely erased, in spite of his attempts to be 'evil'.
However, he's still evil enough. Prideful, brutal, and not accepting any slack from his subordinates. Despite this, he's still good natured enough to his subordinates to keep their undying loyalty. Though, those that do start to question him in any way tend to be too fearful to ask, since he often does his best to show off how powerful and dangerous he is, keeping his soldiers in line in turn.
Ironically, despite his tough facade, Bowser's surprisingly open-minded. ...TOO open minded. Shunned from a young age, he often had to figure things out on his own or through the help of Kamek, neither of which having had parents to guide them in life, and not exactly being allowed in most social circles. Sure, they trained hard using all the records of magic and strength training they could manage(minus the strength training for Kamek, whom focused more on magic). But, regardless of their intellectual smarts and tactics, being so shunned prevented them from learning 'street smarts', leaving them quite naive and easily tricked.
Despite the societal naivety, he actually grew up to be a mighty leader, one able to earn the respect of his forces, not through psychological cunning, but through hard work, military tactics, and adaptive creativity towards using whatever resources are available or nearby.
Eventually, after proving his strength in ruling over the Koopas and the allies he had gained, they tried to gradually take over the kingdom again, in memory of his father. But, the attempts failed, forcing them into exile into more inhospitable lands(where he created the earliest Bowser Castle). But despite being exiled via the power of the fledgling princess, he didn't let that put him down, and he instead used it as incentive to push his forces into training and preparations like never before, organizing them into a militaristic powerhouse of an army.
And it is as he proves himself and builds up his army, and his seemingly restored Koopa Kingdom, that Kamek finally decides to show his master the message from his father about the princess, Kamek having, like his mother said, saved showing it to him till he thought he was strong enough to be ready to oppose the Mushroom Kingdom. Considering the fact that Peach's unintended purification weakened the Toads so much, he decided he was ready honestly earlier than anticipated.
Bowser is at first furious that he hid the message from him for so long, stating that the princess has been with the Toads for all these years, but Kamek says that his mom knew he'd charge in and get himself killed if he did so before becoming strong enough. With how much he's been building his army and his own strength, it reminded Kamek of that promise he made years ago. And with the Toads having gotten so weakened over the years, he should be able to complete that task his father's last will gave him easily.
And that he does. Kidnapping Peach is a breeze for him against the, by then, heavily weakened Toads.
Unfortunately for him, the sons of his father's feared rival were on the job at the time, and were quick to follow, despite the outposts Bowser set for his army on his way to and from his assault of Peach's Castle.
After capturing her though, Bowser was surprised when he learned that she empathized with him, and that his forces were only banished out of necessity, not her personal desire. She had no ill will against him, but she had to protect her subjects. More surprisingly, she had heard, to a degree, tales about him and his father, and empathized with him. And though it was unrequited, her empathy for his plight caused him to fall for her.
During the time Mario was making his way to her to save her, a good portion of Bowser's time spent was used trying to make Peach his, to make her fall for him. Cause when he realized he loved her, he remembered the times of the past, the good moments between himself and his parents before they died. And also how his father was so proud of him, wanting him to inherit their land once reclaimed from the Toads.
In memory of this, Bowser himself found a deep need to gain himself an heir, wanting to gain an heir through Peach, with her as his queen.
...and when he thought he finally figured out a way to successfully win Peach's heart(which would have failed miserably, though he didn't know that), Mario showed up and saved her, much to his fury. And were it not for Kamek's and his safeguard method of dabbling in necromancy, the encounter with Mario would have killed him.
After being brought back to life from the yet to be perfected Dry Bowser state that let him survive the lava he fell in, Bowser entered a bout of depression over having lost Peach. His chances for the family he desired squashed.
Seeing his master's depression, Kamek delves into his research, wanting to help his 'master' that he's helped raised, even if it means going into the forbidden arts section of what they were able to recover from the humans that once reigned over the land.
It wasn't long till he found what he was looking for, in a semi-forbidden section. Spells reserved for only being used when necessary.
What he found was a revision to an old spell used to help those that could not conceive their own children. Before the Mushroom Queen showed up, a revision had been made, for helping the rare few cases of Koopa/human relationships in regards to helping them have children.
With this spell in hand, he needs two targets to make a child through the spell. While Bowser's still grieving over his lost chance with Peach, he gets plenty enough essence from him, enough to use the spell more than once. But, to create heirs for his beloved master, he'll need more.
Unfortunately, he doesn't have any options that can match Peach in potential power, so he'll just have to make due. Experiment to see what results he can get with other sources. Bowser has plenty of types of troops, so he just needs to use some of their essence for them, while making Bowser's dominant so they all wind up as Koopa's. The resulting spell creates the first group of Bowser's kids that are quite well known to the fandom of Mario, utilizing various other troops like Twomps, Chain Chomps, Boos, and more as the other essence part of their creation.
When Kamek brings the kids to Bowser, already pre-aged partially as part of the adjustment to the spell, he thought Bowser would be proud to have heirs to call his own. Unfortunately for Kamek, at least at first, Bowser was royally pissed.
Bowser lived his life as an orphan. Hearing that Kamek went behind his back to create these kids, without even keeping record of whom he took their essence from, pissed him off. They're essentially orphans with no parents, created not from true love but from Kamek's spell. How could the kids have a loving family like that? Bowser had such a family back then, and to hear that Kamek did this without any guaranteed way to care for them, just assuming that he'd take care of them, really pisses Bowser off.
Ironically, his raging on Kamek gets the kids to join in, impressing Bowser. After calming down thanks to that, Bowser decides he likes the kids. Perhaps Kamek's attempt wasn't so bad after all, he thinks. After a moment, he thinks that though he can't compensate them for being motherless, he can at least take the place of being their father figure. After all, in a way, he sort of is. Even though that sort of means that he and Kamek... Bowser shivers at that thought, preferring to not even let such things enter his imagination.
Speaking of them needing a mother, he then remembers Peach. She'd make a great mother. And now, he has even more reason to obtain her once again. And this time, whether he woos her or not, he can still get a powerful heir from her with Kamek's spell. He'd rather win her over, honestly... but at least with Kamek's spell, he can ensure that he won't be left empty-handed should he fail again. Better safe than sorry with those damn plumbers around, after all.
With that, and having seen the kids in action, he takes them for a round two of kidnapping, having Kamek store some of his and Peach's essence in the process, just in case his attempts to woo Peach fail.
Needless to say, attempts to woo fail. And this back-up plan of using Kamek's spell... results in Bowser Jr. Though this time without the time acceleration. Bowser wanted to raise him from scratch, or as close to it as the spell would allow.
The rest is history.
Though on a side note(since I've been researching it lately), only way that the pipes in Bowser's Inside Story could work is if they're magically linked to their components, whether they're broken or not. Which is possible if they were magically turned into pipes from the landshrooms' remains.