Setting: Hyrule Kingdom. Goddess Sanctuary Orphanage.
Purpose: Explain the plot hole caused to the Zelda timeline by A Link Between World's backstory.
Summary: When his talents are discovered by a Hyrulian General, Link is tasked with a secret mission for the aid of Hyrule... but things are not as they seem...
Zelda: Childhood friend to Link, introduced by her aide and fellow childhood friend, Impa. Later reveals her general's treachery in using Link.
Link: A practicioner of the Goddess Sanctuary's beliefs of the goddess's virtues of Power, Wisdom, and Courage, as well as the soul strengthening powers his training has granted. And recognition of his talents during a sparring match leads to getting involved in a struggle that'll change Hyrule itself.
Special Features for Link: For this game, Link's special talents are based on how energy enhanced the size and range of his spin attacks. For this, Link has learned to channel his power into his body and tools to enlarge and enhance them after he's had the time to charge up for such. This allows for various capabilities. For example, enhancing his legs for a super jump. Enhancing his hands to carry or push large objects. Or enhancing attacks in various ways as well, such as being able to send out an energy slash to cut things at a distance.
Plot Points: WARNING. MAJOR PLOT POINTS AHEAD.
The game begins as Link awakens to the Goddess Sanctuary Orphanage as he prepares for his usual soul training, both in regards to meditative detection and using energy manipulation upon the environment.
During his training, he inadvertently knocks Impa out of a hiding place, much to her embarrassment. She says she came to make sure he remembered to come to their meeting with Zelda, but didn't want to interrupt him. One of the onlookers from the orphanage say that's not the only reason she didn't interrupt him, a quick glare from Impa quickly scaring the little scamp off.
Shortly after, they meet up with Zelda for some relatively peaceful recreational activities. But, during it, they get interrupted by some guards wanting to test their skills against Impa, stating they'll beat her this time. She welcomes the challenge... and quickly beats the group of guards. They say it's impossible to beat her... which she laughs off, stating that she's fairly tied in matches against Link, and he's never used a weapon in their sparring matches.
Disbelieving of this, the guards state to prove it, leading to a match against Impa with just his soul training to fight with. And in the middle of the fight, a general gets interested in the fight. General... Ganondorf.
He sees Link get beaten by Impa... but then, impressed, makes a request to see a true match, with Link being properly equipped, asking the guard to bring Link to the armory to get properly geared for a rematch, using any weapons that catch his attention. It doesn't take long for him to come out with just a shield and sword to fight with. He's also granted some training dummies to practice against, him learning how to mix his soul techniques with the sword techniques suggested by the guards at this time before the rematch.
After practicing, Link is able to easily defeat Impa with a block and counter strategy, much to everyone's surprise. They thank Link for such a great show. He's suggested to join the guards, but he displays indecision to the offer, at which Zelda just suggests to spend some time to think about it.
Later that night, Link gets a surprise visit.
Said surprise visit, is a group of soldiers in armor, their faces hidden in the confines of their uniforms. They have come to request Link to come to a private meeting with the General. Link, not sure what's going on, agrees.
After getting there, General Ganondorf meets with Link. He informs him that in recent years, many of the apprehended thieves' guilds' members have gone missing, and yet, their mark on Hyrule has yet to leave as burglaries continue. It's obvious someone within Hyrule's guard is helping them, but at the same time, Ganondorf states the reverse is also true, and he's learned a dire truth from his sources.
Apparently, the guilds have joined together under one leader, and that leader seeks the keys to the Sacred Realm, where the seven sages of the past had sealed the Triforce after the Legendary Hero defeated his namesake, Ganon, the Demon King... the one whose actions made it incredibly hard for him to prove to Hyrule his name was not an ill omen of his return.
Shaking himself out of the mentioned reverie, he returns to his point for bringing Link there. He has seen Link's potential, and would like to put him on a secret mission to acquire the keys before the thieves do and bring them to him. Link agrees.
Before he leaves though, he tells Link that this mission is to remain a secret, even from the castle staff, like his friend Impa. After all, they do not know where the leak to the thieves guild is, and no matter how much he trusts her, the less who know of his mission, the less likely it'll reach the leak. Link agrees, begrudgingly, before leaving, intending to start his mission the following morning.
When waking the following morning, Link overhears from the other orphans in the sanctuary mention about a Great Fairy hidden nearby. The Great Fairies were servants of the goddesses... and since the pendants that open the gate to the Sacred Realm is also related to the goddesses, it stands to reason the great fairy might know something, so he goes there first. Gets the usual game companion there along with directions to the first pendant.
From that, Link has to pursue the pendants while throwing off suspicions by Impa, all while he hears word that Zelda's suddenly been keeping strangely busy due to sudden increase in problems in Hyrule.
As Link heads off to the final pendant, Impa has by then realized that Link is for some reason seeking out pendants(possibly either due to him dropping it or by his fairy partner mentioning it), and goes to talk to Zelda about it as he leaves to go get the third one.
When Link gets back with the third pendant, he finds the castle under assault by thieves.
In the commotion, a group of heavily armored soldiers intercepts Link and guides him secretly to General Ganondorf... but Zelda spots this happening from a distance, and pursues, Impa following close behind due to having been helping keep Zelda safe as her aide.
Zelda, Impa, and a group of soldiers cut off Link's path after anticipating where the soldiers were taking him, demanding him to explain. After explaining, they realize they've been had.... at which point, the soldiers that guided Link, along with... the soldiers meant to keep Zelda safe suddenly shift, their eyes glowing. They quickly deal with Zelda, Impa, as well as the remaining soldiers instantly in a backstab maneuver, one Link barely blocks in time.
Afterwards, after a quick fight... they discover the soldiers that backstabbed them weren't really soldiers at all, but rather, just empty suits of armor controlled via energy.... energy that they see is being pulled towards a single source that walks right in on the group. General Ganondorf, laughing at how well things have gone.
Realizing that the soldiers they were with were just golems controlled by him, Zelda believes and states that he had used sorcery to make golems to impersonate the soldiers and trick them.... He just replies that she's correct, in a manner of speaking.... but it doesn't matter the technicalities, for now Link has brought to him exactly what he needed... the pendants. And thus starts an outside-of-dungeon boss fight.
After the boss fight, it seems as if Link has won. As Link approaches the fallen Ganondorf though, he is suddenly blown back... by an aura blast. Ganondorf stands up and reveals that he is also a former pupil to Link's master, and now, he no longer has to hide it. With that, he easily whoops Link's butt, whom has yet to finish his training.
Next thing he knows, Link, Impa, and Zelda wake up to the land covered in darkness, and a bright light coming from the nearby castle. They rush in to find all the soldiers knocked out or killed, with a clear path leading to what is revealed to be the entrance to the Sacred Realm(haven't decided what the royal family disguised it as yet).
Together, the three quickly enter after Ganondorf, only to see him standing triumphant, standing with the Triforce floating between his palms as its energies begin to finish pulling into him, the sheer force of his aura keeping them from nearing him.
As he revels in his power, Ganondorf says that he's no longer just some meager servant to the royal family.... No, he's more, far more... And as he's stating this, he begins to transform, before announcing himself as Ganon, King of Darkness.
However, he knows that his conquest has only just begun, now that he has the Triforce... and he knows not to be complacent. He knows full well about the threat of the seven sages and how they sealed his namesake, and how they no doubt have decendants. However, he also knows how the Triforce can grant wishes as well. So...
With that, he makes a wish.... grant the sages unawakened successors the same fate that they granted his namesake. He wishes the unawakened sages to be sealed and scattered across Hyrule. With that, they won't be able to gather their powers to defeat him.
Aiming to stop him, Impa tries to leap at him with her sword drawn.... Ganon grins evilly as the unexpected boon of her attack being stopped occurs, as she and Zelda, right before their eyes, get sealed in crystal. Ganon laughs out loud at his luck, two of the sages sealed right in front of him. How delicious irony. Link watches in horror as their crystals are sent flying out of sight to unseen corners of Hyrule.
As Ganon looks at Link, he smirks, stating that he has Link to thank for all of this... so as repayment, he won't kill him. With a smirk, he states: "Get out of my sight." And with a gust of darkness, he's flung clear out of the castle and knocked unconscious.
When Link awakens, he's apparently been unconscious for days. He was found by Sahasrahla, Impa's father.
Apparently, Link has been unconscious for a while, and in the time he's been out, Hyrule has succumbed to Ganon's tyranical reign. Monsters have flooded the land, and Ganon's thieves, whom have been empowered by his powers, have taken control of all the land in his name.
And worse, Sahasrahla says there's no signs of his daughter or the princess anywhere. At that, Link explains what happened, which troubles Sahasrahla... but he tells Link there's still hope. He asks Link if the pendants glowed for him when he acquired them... when he says they did, then he says it's as he thought. With them, he can get the Master Sword from the Lost Woods, and with it and the pendants, find the sages.... But right now, to do so means he'd have to sneak back into where the entrance to the Sacred Realm is.
Ganon may have abandoned the gateway for his new Phantasmal Palace floating nearby, but it's still near his territory, and thus heavily guarded. He'll have to sneak through to regain the pendants there.
Basically, a 'don't get caught by the guards' scenario, since without the Master Sword, Link will be unable to damage the empowered guards.
Afterwards, and perhaps a mini-boss fight, Sahasrahla guides Link to the Lost Woods, telling him he'll await his return once he has gotten the Master Sword, perhaps even giving him a gift to help through it or something. Perhaps a better shield or something that'd help with some enemies there, stating he deserves it due to having earned the honor of wielding a true soldier's gear. Or something else. Not sure on what to have him give yet.
Anyways, after returning afterwards, Sahasrahla teaches Link how to use the Master Sword with the Pendants together. Two pendants float up above the sword forming dual triangles interconnected, while the third, the pendant of courage, wraps its strap around the hilt before pulling in the direction of the nearest sealed sage, acting like a compass, setting Link on his journey.
Meanwhile, when Link pulls the sword, Ganon senses it, and deciding to make it harder for them, he uses his powers to turn the seals into their own defense, using the sages' own powers and nightmares to fuel it, he creates new fortifications around where the seals have been placed, brought to life through his Triforce.
Through these nightmares and its effects on their fortifications and the nearby area lead to Link learning more about each Sage as he goes to save them. But, for a plot twist... each boss in some way has the sage's seal crystal in the room, and before you can defeat the boss, Link must find a way to cut the spiritual link that the boss has to the corresponding sage utilizing his spirit powers that he has in this game, and doing so merely gets the battle truly underway as it forces the boss to take on solid form.
Eventually, each of the dungeons are defeated, and the defeat of the bosses turn them into ruins of their former selves, leaving just enough room to traverse them should you have missed any items there.
Anyways, after that, with the sages' help, Link can enter Ganon's castle. And while there... instead of having to free the sages, he must lead each of them, down different paths, to the boss door while finding a way to open it.
Eventually, they make their way to Ganon, who though impressed, thinks they stand not chance against him with all the power the Triforce has granted to him. So, he decides to toy with Link a bit... while Link has to get the sages into position and protect them long enough to tear the Triforce from Ganon.
Eventually, the sages pull the Triforce from him.... but Ganon won't let it go without a fight. His attempts to keep it split it in three. After a bright flash, two of the pieces get pulled to Link and Zelda, but Ganon prevents the third from escaping.
In a rage at having suffered from underestimating them, he decides to split them up, so that he can take down Link personally for all his interference he has caused... interference that has cost him the Triforce.
In this rematch, Ganon decides to take things seriously, utilizing his aural powers to their peak, even summoning copies of himself or using it for various explosive aura strikes. But, thanks to the Triforce of Power, unlike Link, Ganon can charge up his aura attacks near instantaneously, allowing him for aural headbutts, aural uppercut stabs from the ground, and more.
Eventually, however, Link manages to overcome Ganon when his own Triforce gives him a boost not in power, but in speed, with Ganon becoming more desparate after Link has awakened this power.
In the end, Ganon is killed, and Hyrule saved, as the legend of the event is recorded for future generations to read about... such as during A Link Between Worlds and how it told of certain key points in this adventure.
Additional Notes: For this, there'd be a love triangle between Link, Zelda, and the younger Impa(around Zelda's age). The relationship would be left up in the air for the players to choose.
Additionally, many of his aura powers that he learns would be utilized in the solving of puzzles. Example, charging up a straight up jump and slashing to reach an out of the way switch. Or charging up an energy slash to cut some ropes on the other side of a pit. Just to list some examples.