The below backstory is relayed in the intro of the game
Many years ago, the Gerudo were dragged into a war with the rest of Hyrule by their King Ganondorf’s obsession to obtain the legendary Triforce.
Ganondorf plunged the land toward darkness and ruin. But as Hyrule teetered on the brink of collapse, the evil King was defeated, the Triforce united, and he was sealed away into a realm of darkness.
Following his defeat, his people, the Gerudo were exiled into the harsh wasteland of the desert, guarded so no Gerudo King could again wage war on the peaceful land of Hyrule.
In the absence of war, Hyrule prospered. The King gained respect with the defeat and exile of the Gerudo, and the Royal Family steadily gained power and wealth.
Many years later, a Gerudo King again appeared from the desert sands. Arriving in Hyrule, he was greeted by the Royal Family’s strongest warriors- but he carried no sword or, it would seem, darkness in his heart.
The new king claimed he’d learned from his ancestors’ mistakes. If his people were to survive, it was time for them to mend their relations with the people of Hyrule.
It was unclear whether the Royalty was more interested in his message or in the marvelous gifts he brought from the dusty lands. But they agreed to hear him.
The camera begins at the grandeur of Hyrule Castle with the Gerudo king (as shown in the prologue) on a balcony, then scrolls down the main avenue for a small ways before moving to the slums. It scrolls up the road to the squalor of the Thieves’ Hideout. Link is asleep in his bed, as per Zelda requirements to have Link asleep at the beginning of the games.
Getting up, Link encounters Farin, his gang’s mentor and father figure. Farin says that Anton is waiting outside, and he’s going to test Link on the thief skills Link’s been learning. Outside, Anton meets Link and, in the area around their hideout, has Link follow him up climbable walls, walk along tightropes, slide along narrow ledges, and hide in barrels. He tries to show Link the barrel ambush where you break the barrel in a spin attack, but Link merely clunks around. Anton says it’s okay, they can practice, when Link’s rival, Sykes, shows up.
Sykes takes the barrel ambush failure as an opportunity to again taunt Link, challenging him to steal things using the pick pocketing technique, recalling that this is something Link has always had trouble with. They go to a square in Old Town and Link manages to steal something from a vendor’s stall, but Link is caught when he tries to pickpocket a rich citizen. Sykes quickly abandons Link, who tries to make it back to their hideout.
The streets are unusually chaotic, with guards everywhere, but Link quickly realizes they are not looking for him. He overhears that Princess Zelda has disappeared on an official visit to Castle Town and the guards are searching everywhere. Entering the slums, he bumps into the princess, who ducked out of the procession, horrified to discover so poor a part of her families' kingdom could exist.
They talk a while, the gracious young princess seems determined to help the poor folk. The Gerudo are suffering in the desert- but how can they hope to reconcile themselves with the Gerudo when the same injustice occurs on their own doorsteps?
Just then the guards arrive, closely followed by the rich citizen who relays the story of Link's crime. He concludes that Link must have also been trying to kidnap the princess. Despite Zelda's protests, Link is thrown in jail.
That night, the celebrated Gerudo king turns up unannounced at the jailhouse and bargains with the guard for Link's release. Unsure of his reasons, but glad to be free, Link goes with him.
The king talks of his people, the Gerudo thieves; how their history of evil kings has caused prejudice and discrimination, and how they’ve been exiled to the harsh desert, burdened not only with the unforgiving climate but also hard taxes and trade embargos. He confides in Link how he hopes to reconcile them with the rest of Hyrule on this diplomatic trip.
- (we need him to indicate that he is not Ganondorf, but supposedly a new Gerudo king who isn’t evil. But srsly it is Ganondorf.)
He tells Link that he heard talk in the royal court of his misadventures and has a proposition for him. This noble gentleman rogue is looking for an apprentice: a naturally gifted thief to pass his skills and his legacy down to. He would treat him like his own son, and be the father to him that neither of them ever had.
Link is tempted by the prospect of living like a prince instead of a pauper, and the chance to learn from a master thief, and a Gerudo no less - that would show Sykes - but he remembers he already has a surrogate family, and reluctantly declines the king's offer. The noble thief is saddened by Link's decision but tells him he admires his loyalty to his friends. Link leaves to go back to the gang's hideout.
He arrives at the hideout to find Farin missing. Sykes tells Link that Farin went to find Link and has been arrested. Link must have turned him in for his own freedom! The rest of the children are intimidated into playing along with the older kid's story and they decide to kick Link out of the gang.
Feeling hurt, angry and rejected, Link returns to the gentleman thief's quarters and accepts his offer of an apprenticeship.
First thing the next morning Link is sent on an errand. He is to take a voucher to town to pick up some new clothes, befitting of a gentleman thief's apprentice. Link picks up a finely tailored green tunic and cap, and changes out of his dirty rags. Before he can leave, the shopkeeper asks him to step into a back room, where there is one last article for his outfit. The shopkeeper hands him some dusty bracers, telling Link he's glad to have these filthy things out of his shop, and sends Link back to his new mentor.
Upon his return Link's new master elaborates on how it is his most fervent wish to see peace restored to Hyrule, but he is beginning to fear it is impossible – although Royal Family was happy enough to welcome him and the gifts he brought from the desert, the Hylian royal family seem as if they will never deign to extend the hand of friendship when it is so easy to let the Gerudo continue to bake in the desert sun. No, if he is to see his wish become a reality he believes there is but one option. He relays to Link a somewhat abbreviated version of the Triforce myth, emphasising its ability to grant the bearer their heart's desire. The king would use it to return peace to Hyrule, to free the oppressed, but the Triforce was long ago sealed away. Locked behind an elaborate clockwork mechanism, the only way to access it is with four cogs, forged for this purpose and imbued with forgotten magic or something. The king had been searching through ancient scrolls in the castle’s library, and believes one cog resides with the Deku tribe.
Link begins to understand what the King expects of him. He is too old to undertake the task himself, but is willing to pass on his considerable thieving skills to Link in return for retrieving the pieces of the puzzle that leads to the Triforce. Enthralled by his new mentor, he leaves Castle Town for the first time in his adventure.
Link goes through Hyrule field and into the Deku Swamp. The swamp, once a thriving environment, is now plagued by poisons. The core of the poison is a monster releasing spores into the forest, creating a thick confusing fog, vile creatures, and turning innocent Deku Scrubs into vicious Mad Scrubs.
In his paranoia, the Deku King tried to protect himself and the kingdom from the spores. His efforts were futile however, and he was exposed to the monster's spores, causing him to act mad. He has sealed up the palace and is ordering the guards to ignore the swamp monsters and just protect him. The Deku are outraged by this and demand a new king, although some remain loyal. However nobody can do anything since the palace is locked up. The Deku village isn't currently affected by the fungi, but is close to infection.
Talking to Deku in the village, Link learns about the situation and can’t find any way into the sealed palace. Three Deku tell him about specific problems. One discusses two or three mushrooms that are growing close to the village and turning any Deku who goes into the fog into a mad scrub. Link ventures out into the fog of the swamp and destroys the fungi. Another Deku is worried about a small party of Deku who went to make a sacrifice to the forest spirits and haven’t returned. Heading to the shrine of the forest spirits, Link finds the party trapped by mad scrubs and other swamp monsters, and by defeating the monsters the party can return to Deku Village. The third upset Deku claims that a witch stole his Deku nuts (wow that sounds like innuendo). Also outside the village, Link finds the bundle of stolen nuts, perhaps he catches a glimpse of the witch flying through the swamp on her broom.
When Link returns to the village after completing all three tasks, he finds that many of the Deku are missing and the palace is unlocked. Nooku and Roiko, the palace guards, are found in a deep sleep on the job. Walking through the open gates, he encounters the witch, Maple. She bumps into him, laughing at the odds of finding another human here. “Whoops! Must have left the gate open! Looks like all kinds of people are getting in here. Anyway, I’ve got a cog to find, see ya later loser!”
Link heads into the throne room to find the Deku (with torches!?) have stormed in and are demanding that the king be sacrificed to the Kokiri spirits to appease them.
Link is surrounded by Deku who consider sacrificing him, although those who he helped are on his side. Suddenly, sound of the swamp monsters sounds loudly and a hole in torn in the wall. Swamp monsters start to swarm in and attack. Link must stop the monsters from getting in, thereby gaining the trust of the Deku. The prince, previously cowering under his father’s protection, is inspired by Link's bravery and takes control of the situation. He asks Link what he’s even doing here, and finding out he’s searching for the cog, the Prince orders the Deku Butler to grant Link access to the Kokiri forest. He thinks the cog got left somewhere in there one time. The butler gives Link a key which unlocks a gate at the Forest Spirit Shrine, along with a gift- the boomerang.
Link heads into the Kokori Forest- a foggy, shifting maze of a woods. Trees grow and twist seemingly on their own. Link will need to use his thief agility to climb trees, and his boomerang to knock out the pesky Kokori spirits who keep changing the paths through the woods. Eventually, he comes to the remains of a village overtaken by the forest, where he sees Maple looking at a decaying doll on the ground, standing next to a hazy, ghostly figure. “So this place used to be full of life, huh?” She notices Link and the ghost disappears. “Oh, shoot, you’re still here? Are you following me or something? Sheesh,” she says, and flies in the direction of the temple. Link has the option to look around the ruins and gleam clues about the fate of the Kokori and perhaps clues about the temple’s puzzles, but it isn’t necessary. He follows Maple to the Forest Temple.
The temple is in and around the decaying remains of the ancient Deku tree; enormous fungi grow up the sides of the rotten wood. He encounters the mischievous Kokori spirit Tilo, and despite/because of her assistance, finds his way to the boss, a monster growing amongst the root system of the great tree and responsible for the fungal growths throughout the swamp. Entering its lair, Link sees Maple thrown out into the forest by the monster. He engages it and wins, of course.
Following the monster’s defeat, Link acquires the Forest Cog, and the fungi in the swamp and forest disappear. The Deku king starts to recover and the prince proves to be an effective leader. Link heads back to Hyrule town to bring the cog to the Gerudo King.
Heading back to Hyrule Town after finishing up in the Deku Swamp, Link goes to meet with the Gerudo King. Arriving at the castle however, the guards tell Link that commoners aren’t permitted into the castle. “Oh, you have a meeting with the Gerudo king? Princess Zelda mentioned you’d be coming. You’re not allowed in.” Not sure exactly why he’s been barred from the castle, Link sneaks in anyway using his awesome thief skills and makes his way to the Gerudo King’s chambers.
The Gerudo King greets Link, glad that he collected the first cog. He’s surprised, however, that Link was barred from the castle. “I’s unlikely, but… the Royal Family has only grown more and more evasive on the subject of repairing the relations between our people. Perhaps one of them suspects you are helping me search for the cogs…. But no matter.” He explains that his research in the royal archives has led him to believe that the Zora and Goron tribes were each given a cog to protect. It may be that the final one is with the Royal Family, but it’s been more difficult to track. He will continue searching for the location of the final cog while Link looks for the next two.
On his way out of the town, Link happens across a Deku merchant making a scene in the square. It turns out that his goods were stolen by a band of traveling Zola. In the field, Link finds the Zola and fights them. Win or lose, the Zola abandon the fight and goods when another Zola arrives and informs them that "hostages have been taken." Link returns the deku merchant's goods, and he lowers the price of his flippers, allowing Link to buy them and access the river valley of the Zora.
Link swims to the Zora settlement, finding everyone panicked and useless, as their leaders have been kidnapped by the Zola and taken to forts along the river.
Either sneaking or battling his way into three forts, Link rescues the prince, princess, and King Zora. The Zola flee their forts after their defeat, opening the path into Lake Hylia.
At Lake Hylia, Link meets a man named Sheldon, who is studying the ancient mechanisms that dot the lake shore. Link goes to investigate one, and finds Maple sitting atop the machine, investigating it herself. “You again!” She says, noticing Link. “You cog stealer! Look, I need these cogs if I’ve ever going to become a great witch. Let me prove myself!” She breaks off part of the machine with a spell and hurls it at Link. He dodges out of the way and a skirmish is underway. After being defeated, Maple flies off. “Whatever, loser. You’re still way outmatched. Those cogs are mine!”
Sheldon sets about repairing it the mechanism Maple damaged, while Link goes to find the rest. He activates each one, and returning to Sheldon, they activate the last one, which raises the entrance of the ancient lakebed temple. Link approaches it, and overhears Maple talking with the spirit Link saw in the Kokori Forest, the Hero's shade. “Yeah, yeah,” she says to the Hero’s Shade. “I know you can’t go in there yourself because of that seal thingy. Just trust me on this one, I’ll get it!” She flies into the temple, and the Shade turns around, staring right at Link. He warns Link to avoid tampering with things he doesn't understand or he could bring the lives of everyone in Hyrule to an end, before vanishing.
Regardless of the hero's warning, Link enters the temple, claiming the water cog and advancing his quest.
On his way out of the river valley, Link is attacked by the remnant of the Zola, wanting revenge for their defeat. However, before Link can fight, the prince and princess of the Zora arrive and defeat the Zola. They share with Link that his courage inspired them to become stronger and take action to decide the course of their lives. They give him the Zora seal or whatever, an object signifying the friendship of the Zora people. This item will evoke different reactions from Zora characters Link meets now.
Link heads back toward Hyrule town...
Anytime after the Forest Temple is cleared, one of Link’s old gang members will be near the market in the slums. Talking to him/her, they say something along the lines of that they’re surprised you’re still in town, Sykes said you ran away because some rich person gave you money for turning Farin in. Well, there’s some other kids trying to form their own gang. They’re posted on a rooftop shooting rocks at us, and we can’t get back to the hideout. Link can use the hookshot to get to this roof and talk to the kid in the rival gang, who’s super intimidated by Link. He runs away, and his friends, who have been blocking off a section of Hyrule Town, go with him. Link talks with his old gang member, who says maybe Link isn’t such a bad guy. He should talk to the other gang members.
Now that the other kids are gone, Link can access an entrance to the sewers. He can follow a path through a drainage pipe and out to a grove in Hyrule field, where the bow and arrow is waiting in a chest.
A short way up Goron mountain, the bow is needed to progress
Link arrives on Goron Mountain to find all the Gorons suffering from a tooth-rotting disease. Mining operations and production of manufactured goods have stopped completely, and all the Gorons merely sit around on the mountain, weakened from malnutrition and depressed since they can't do basically anything.
Link finds the Goron Elder, Gor Indigneo, ensconced back in his chambers. Upon entering, he is angry to see a mere Hylian has gotten in, and demands to know what Link wants. Upon hearing Link wants to search for the Earth Cog, Gor Indigneo gets even angrier. He explains the problems the Gorons have: their teeth have been rotting ever since they discovered the Violet Ore, his people are weak because they can't chew rocks, they have to eat mud soup made from mushy ore mined down the mountain. My people are eating mush! There's no calcium in mush! The Gorons are strong people, and maybe could get through this, but the worst thing of all is that the Gorons are all so depressed they're beginning to give up hope that anything will ever get better. The last thing we need is some Hylian trying to find some ancient artifact when we're trying to deal with our own problems! I can't help you until my people's happiness is restored! Guards, take him away! The Guards rise slowly, pause for a moment, then sit back down, too weak to do anything. "See what I mean? Get out of here!" the elder screeches.
Link wanders around the village, and while talking to the Gorons, two or three mention that they miss the old days, before there were problems, when the simple pleasures were watching a good Goron wrestling match. The old wrestling arena sits decrepit and decaying.
Link can find an old wrench hidden somewhere around the Goron settlement. If he brings this to the Chief Smith in the Goron forge, he will recognize it as his favorite wrench, which he lost years ago. He thanks Link for bringing it to him, and says he sees Link is a pretty handy fella. Maybe Link, just maybe, is the person to fulfill the Chief Smith's dream- of restoring the wrestling arena. He'll give Link four or five bolts, and tell Link to patch up the failing supports.
The wrestling arena is actually suspended above a canyon. It is anchored in four or six places, on different levels. Link must use his agility to climb to the places where the supports are failing, and attach bolts. The last touch is tightening the chains that wind around the ring and serve as railings. After fixing up the arena, some Gorons around town, including the Chief Smith, will notice, and mention that they miss the old Champion Wrestler, who moved out of town after losing his strength to the Violet Ore disease. Link explores the mountain, and following a winding trail, he finds the home of the old Champion (I'm just gonna call him Champ for now). He spends his time throwing small rocks (he can't lift heavy ones) at a nearby rock wasp hive that's been bothering him for a few weeks. He won't talk to Link, saying that he's too busy to talk to small fries.
The hive is inaccessible by foot, but Link can shoot a nearby bomb flower, which will explode and destroy the rock wasp hive. After this, Champ will talk to Link, with a small amount respect. Champ calls Link smart guy, commenting that maybe Link doesn't have brawn, but he does have brains. What? Go back to wrestling? Look smart guy, maybe you didn't hear, but all the Gorons are weak, weak, weak. We don't get the nutrients we need from the mush soup. Anyway, the arena is falling apart. If Link has restored the arena by this point, Champ will think about it for a minute. "Well, maybe it would cheer my brothers up... Alright, I'll do it. But you've gotta fight me."
If Link agrees, the player will find himself in the arena, facing Champ. All the Gorons have gathered around to watch. All the buttons only make Link punch (which is probably just the sword animation without the blade), but he can still use agility moves. Champ is actually pretty fast, but not as fast as Link. He will block any punches Link throws at his front and counter. If Link stands still, Champ will punch at him. If Link can get behind Champ and hit his back three times, Champ will sit down and surrender. If Champ hits Link three times, Link will loose.
Whoever wins, Link and Champ stand facing each other outside the arena. Champ tells Link that was the best match he's had in many years, Link is pretty fast. All the others Gorons will cheer, saying that it was fantastic to see another match. Look, Champ is still fighting even though he's sick. Maybe we can all fight! We're all still champions!
Link goes to see Gor Indigneo again. He admits that he's heard everybody loved Link's fight with Champ. So is this what you do? You help others to serve your own ends? Well, I do know where the cog is. We left it deep in the Violet Mines before they were shut down. I'll send word for Gumbo, who has the keys to the minecarts, to let you go there.
In the dungeon, Link encounters Maple again. “Weird hat guy! I should have known I’d run into you here. Are you tied to my broom with rope or something? Look, you’ve already got three of the cogs, can’t you at least let me have one? I need their power… I mean, if Gram’s ever going to accept me as a real witch… That ghost guy keeps telling me how important it is… I just want a cog.” She starts to fly out of the room sadly, then decides she’s angry at Link. “So stop trying to take all the cogs! You’re not a pocketwatch, you jerk!” And she casts a spell, strong monsters appearing or the lava rising or something. “Oh, oops. That’s a bit more than I meant to do… Hey, I’m getting pretty good.” She flies off.
Later, Link and Maple find themselves together in the boss room when they're attacked. Working together, Link and Maple take the boss out. Afterwards, Maple swoops in to grab the cog, but then pauses. She realizes that before, she never would have had the courage to face that monster. She's grown a lot, even without getting any cogs. She doesn't immediately hand the cog over to Link, though. She gathers a vial of venom from the boss, and using the cog's power, she synthesizes an antidote for the Goron's tooth rot disease. She gives it to Link, then says she needs to go back and talk to someone. She goes back to Syrup to finish her witch training.
Link brings the antidote to the elder, who gives it to all the Gorons and cures them. The elder admits that maybe getting help from other people is a good thing, and the Gorons actually need it from time to time. He reminds Link to make sure he gets help when he needs it too.
Link returns to Hyrule Castle and sneaks past the increased security to find his master. The Gerudo king is pleased at Link’s progress and congratulates him on the three cogs he has acquired, complimenting him on how strong he’s grown. As for the final cog, the king has been digging deep into the royal archives and believes that many years ago, the cog was taken from the castle to be protected by the royal family’s servants. “Perhaps you’ve heard of them. They are called the Shadow Folk. The Sheikah,” The king says.
“After a war between my ancestors and the Hylians left my people exiled in the desert, the Sheikah were tasked with guarding the path back to Hyrule so we might never return. Their icy resolve to their duty was almost as crushing as the unforgiving heat of the desert. With them lies the final cog.” He presents Link with a key. “The Sheikah fortress lies at the desert’s mouth, at the end of the Valley of Death. The valley is closed off, but you may be able to sneak in. This key is ceremonially given to the messenger to the Shadow Folk. I’m afraid it was unceremoniously taken from him. Now you are the new messenger. Be careful. ”
As Link starts to head out of the castle, the King stops him. “Be wary of the Sheikah. Their cruelty has kept hope from the Gerudo’s eyes for generations. But be even more wary of the desert. Under no circumstances enter that dusty land, for there is no returning.”
Link finds the entrance to Death Valley, which is blocked by a gate. Using the key the Gerudo king gave him, Link sneaks into the gatehouse and opens the path. He trudges through the misty treachery of Death Valley and eventually finds himself at the gates of the Sheikah fortress, the walls of which completely block the pass through the mountains. As he holds the Shadow Key, he is allowed in and goes up the tower where the Sheikah elders meet. But upon finding out his errand is to collect the cog from them, they scoff. They know what the cog is for, and they certainly aren’t going to give it to Link. He’s thrown out of the tower.
Link is unsure of what to do now, there are no leads to follow. Outside the fortress, he catches a glimpse of a figure headed away from him. He follows it, along the top of the fortress wall (or perhaps along its base.) When he catches up to the figure, it disappears. Then it reconstitutes behind him as the Hero’s Shade and attacks. Link fends the Shade off, as it tells Link “your quest ends here. You’ve brought Hyrule to the lip of destruction and it’s teetering in the wind. The cogs mustn’t be brought together.” During the fight, Link is knocked off the wall and into the desert (or else hit very hard and knocked through a weak part of the wall into a tunnel in its foundation). The Hero’s Shade stands looking after Link, but doesn’t chase him. “This desert breeze. Perhaps it is the wind of fate.” Or something. And he disappears.
In the desert, Link is captured by the Gerudo. The Gerudo initially seem beat-down by the Sheikah, and Link sympathizes. They’ve been forced to live in the harsh desert, taxed by the Hylians, denied trade. But the Gerudo don’t trust him and aren’t sure what to do with him, so they take him back to their town and throw him in their jail. He escapes from the cell and sneaks into Abigail’s quarters, the Gerudo leader. However, she catches him. But she admits he’s got spunk, and they strike a deal. The Gerudo have made a discovery, and might be able to use this chance to finally get out of the desert and let those Sheikah know what’s what, fight for their freedom. Link will help them because he likes helping people, and because helping them attack the Sheikah will allow him to get close to the cog. And because the Gerudo are kind of making him, I mean, he’s their prisoner.
Link is to go to one of the old Sheikah outposts, long abandoned. Fighting his way through traps and creatures, he finds the Fire and Ice Arrows, left there by the Sheikah. He brings them back and turns them over to the Gerudo. Abigail explains to Link that the Fire and Ice arrows were designed by the Sheikah and are used as a key on many locks in their fortress. Now that the Gerudo have gotten a hold of them, they can get past the Sheikah blockade.
Link is given the task of gathering some weapons from the storehouses. Inside one of the storehouses, Link finds a memorandum left by a Gerudo. It’s a directive from Abigail indicating that no Sheikah are to be left alive, no mercy is to be shown, etc.
It suddenly sinks in what Link has helped set in motion. As he stands, kind of shocked, a Gerudo walks in. She can tell from the note he’s reading and the look on his face that he didn’t realize what was going on. “The Shadow Folk have been forcing us to eke out a life in this desert for generations with no support. Do you think everyone’s survived that? It’s been a war, it’s just our chance to attack now. What’s what look? You don’t want all the Sheikah to die? Are you going to stop us, then?” The Gerudo draws her sword and attacks Link.
Link defeats her in battle, but coming out of the store room, the Gerudo have already left. He heads to the Sheikah Fortress, which he finds under attack by the Gerudo. Fighting his way through both Gerudo and Sheikah, he sees Abigail heading for Seere. He chases her through the fortress eventually to a path leading to the temple. Using Fire and Ice arrows, Abigail and Link are able to unlock a number of doors leading through parts of the fortress that haven't been opened for years, some parts crawling with Redead.
If you helped more Gerudo/got in the way of more Sheikah, then the elder will call upon his body guards, and Abigail will say, ha, it seems they've busy losing the battle. Or in the other case, the elder will say, oh so you came alone? Or did all your reinforcements lose to my warriors? Either way, they'll start to fight, and Abigail will shoot a fire arrow Link's way, burning down the path to get to them to interfere.
Only one path remains for Link, which is in the direction of the Temple entrance. When he gets there, he is confronted by Seere. He talks to Link, saying that he's seen him in visions. He might bring great destruction, or salvation- only the path of shadow will show the truth: and he opens the gate to the shadow temple, and pushes Link in- initiating the first battle with the boss, which Link can't destroy, but can fend him off.
Eventually, Link exits the Sheikah dungeon with the last cog finally in hand, only to find himself face to face with the aftermath of the Sheikah and Gerudo's battle. Seere, standing nearby, explains the situation to Link. "[whichever side you helped more] seems to have won. But both sides suffered heavy loss. We've lost too many warriors to hold the pass, but the Gerudo are retreating due to their casualties. I don't blame you for this, you just added a spark into years and years of kindling. In fact, I'm still not sure whether you're destroying Hyrule or bringing about the healing we've been needing for ages. But that's just me- there are some Sheikah who definitely blame you for this. Oh! Here they are!" And several Sheikah warriors jump into the scene. The player is prompted to run.
Link scrambles across the rubble of the fortress, climbing collapsed walls and still-burning timbers to escape from his pursuit. He eventually loses them in the mists of Death Valley. Link returns to Hyrule castle to meet with his mentor and finally present the cogs.
The security measures at Hyrule castle have been increased multiple times to keep Link out, but he climbs and sneaks his way up to Ganon's quarters, finding the king waiting on the balcony. He turns and congratulates Link on collecting all the cogs, there is only one thing left to do before they can find the triforce and return balance to Hyrule. But before Ganon can go on, a shiekah warrior jumps onto the roof, demanding the return of the cog before hyrule is destroyed. Ganon promptly refuses, saying it's time the triforce belonged to someone who'd use it, and attacks the Sheikah.
Working with Ganon, Link takes the Sheikah warrior down. Ganon raises his sword to deliver the final blow, but before he can end it, Zelda appears. "Well, Princess," Ganon growls, "it seems you've arrived just in time to discover that the once-loyal Sheikah are now attacking allies of the royal family."
"Sheathe your sword, pretender" Zelda replies, turning to Link. "Link, I found a prisoner who had escaped from the dungeons lurking around the castle's library. He and a few friends want to talk to you." One by one, Link's gang arrives on the roof, followed by Farin. He apologizes for not being there for Link, but it's time Link found out the truth: Ganon isn't the Gerudo king, he hasn't even been seen by the Gerudo in 300 years. Ganon in an ancient villain who has returned to finally claim the triforce by manipulating all of us, including you, Link, and including me. Ganon framed me for murder seven years ago, forcing me to leave my people and abandon my throne. Ganon is a villain who wants nothing more than the triforce, for his personal gain! I am the true king of the Gerudo!”
Ganon maintains his facade to the end, however. He brings up how he accepted Link when his gang spurned him, how he gave Link a purpose when before all Link did was steal from others for his own good. Together, they can still claim the triforce and save Hyrule. Link looks back and forth between each party. He eventually steps toward his gang. "Ah, so this is how it will be," Ganon says. "That's fine, you've been a weak pawn recently, wasting precious time to rescue the Zora royalty or cure the Gorons. If you'll allow me to take back what I've so graciously allowed you to use, I will bestow them on another pawn." Ganon uses magic to rip the cogs from Link and they float to him. "Thank you for your help, but only a fool holds onto tools after their usefulness is past"- and he pulls back his sword to attack Link.
Farin immediately jumps in front of Link, taking the blow. Ganon whirls back, laughing, then strides into the castle from the balcony. Zelda and the gang rush to Farin's side. Zelda inspects the wound and says that she'll have someone attend to him, and he'll be fine, Ganon was aiming much lower than your vital organs. Farin admits that's good news, however, Ganon escaped with the cogs.
The Sheikah suddenly warrior gets up from the corner where he'd been kneeling, surprising everyone who'd kind of forgotten about him. He says he knows where Ganon will head: He'll use the cogs to open the Celestial Clock, the vault that's housed the triforce since the last time Ganon tried to steal it. However, there's still hope- Ganon can't do it himself. Zelda agrees, saying she'd read about ancient magic that prevented anyone who'd ever touched the triforce from removing the cogs from their resting places. The Sheikah says Zelda is right- and the same spell prevents those people from entering the Celestial Clock. "Doubtless, Ganon's hatched some scheme to get in anyway," Farin interjects. "We must stop him." Zelda tells Link that she needs to get someone to attend to Farin (dude stop bleeding all over my castle), but Link needs to run ahead to try to stop whatever is happening, Ganon cannot get his hands on the triforce or Hyrule will be destroyed.
The player is now free to rush into the next dungeon, but all the gang members, Zelda and Farin can be spoken to. If you speak to Farin here, he'll mention some of his backstory- he was born as the King of the Gerudo, but before he came of age, Ganon framed him for murder. He escaped his execution with the help of a Gerudo witch named Syrup, but both had to split up and flee the desert. Farin was wounded during their escape, but he was found by a Sheikah hermit and nursed back to health, and he eventually tracked Ganon to Hyrule. He's been gathering information and waiting for the moment to expose the king. He should have told Link about all of this, he's so sorry.
Talking to Zelda will explain what's happened with the good guys since the beginning of the game. She apologizes for not trusting Link with her suspicions of Ganon, but to be fair, Link was working for him. She never fell for the bribes of treasure, stolen from Gerudo temples, that Ganon lavished on the royal family. And when she found one prisoner in the dungeons, Farin, who seemed to know that Ganon wasn't who he said he was, they started gathering information from within the castle. That's how they found out about the cogs and celestial clock, legends largely forgotten by the royal family.
The player should have had the option of interacting with the gang members already, so they just encourage Link, and apologize for kicking him out when Sykes told them he betrayed Farin.
Link runs to the entrance, only to find the cogs have already been placed into the door and the temple has already been entered. As he walks by the doors, he pulls the cogs out to continue to use their power (or maybe he doesn't. We'll have to decide, gameplay-wise, since we'll probably not want to rob the player of abilities they've been amassing right before their final battle.), and steps into the final dungeon, the Celestial Clock.
Inside, Link keeps catching glimpses of a mysterious figure ahead of him. Every time Link almost catches up to the figure, it sets off a trap to block Link.
Link finally catches up in a room empty except for a single sword enshrined in the center. The figure turns around and reveals himself as Sykes. "Surprised?" He asks Link. "I thought you'd understand. Back when everyone in the gang turned their back on you, you just found someone else. Well, the whole stupid gang decided that you're okay again, so they turned their back on me! But Lord Ganondorf saw that I was worthwhile. He's been training me to become a better apprentice, so I can finish the mission you couldn't! Want to try and stop me!?" With that, the temple's mini-boss battle against Sykes commences.
When Link wins, Sykes sits down and pouts. "All I ever wanted was to be accepted. I just want people to like me! And now look, everyone's turned against me, not even Lord Ganondorf would come into this maze with me. And I can't even pull that sword out of the pedestal!" Link walks up to the blade and gives it a tug. The room swirls around him and he is engulfed by a white light. In front of him, the Hero's spirit appears.
"We cross paths again. But this time, I am not your enemy. Ages ago, I enshrined this sword here myself. It is the pin that binds an old spell- a seal preventing anyone who has touched the Triforce from ever entering this dungeon -only a true Knight of Hyrule can remove it. I guess you weren’t so bad after all. However, now that you have broken the spell, Ganondorf will be on his way here to collect the Triforce. But Ganondorf isn't the only one to step out of legend and back into Hyrule's fields. Accept the gift of the hero of time!"
And with that, Link and the hero merge. The white light fades, and Link swings the master sword. The really cool attack that the Hero has been shown to use is now available to Link, and will come in handy for the rest of the dungeon. The hero's voice echoes through the chamber- "Now claim the triforce for the side of light!" Link looks toward the door he didn't come through, which now opens. Naturally, he goes that way and gets through a couple more rooms to the end of the dungeon. (Sykes keeps sitting in the corner pouting about nobody liking him. You can try to talk to him, but he'll just snub you.)
Link reaches the end of the dungeon, but as he steps into the room at the heart of the clock, gears clicking all around, the face of the clock towering over him, Ganon steps in behind him. He thanks Link for helping him get this far.” Any who have felt the light of the Triforce under their fingers are barred from the temples. A clever spell, but not one our teamwork couldn’t overcome. But I see you’ve joined the other team. You seem to have inherited the spirit of the hero of time. Once more our destinies cross." And with that, the showdown for the triforce begins.
The Final Battle and Conclusion
After a couple phases of the battle, Ganon will, typically, power up or something. Link doesn't know exactly what to do until Sykes shows up. He says that he's always been better at stuff then Link, so maybe Link could use some help. "After all, helping people... I guess that's why everyone likes you and not me, isn't it?" And the final phase of the battle is accomplished with Sykes' help.
The two outcasts defeat the king of thieves through their teamwork, and as Ganon collapses, Zelda, Farin, and the rest of the gang step in. Zelda, Farin, and Link form a triangle around Ganon's form. Zelda nods to Link and on her signal, the three of them do some magic thing that takes Ganon away. And at that moment, deafening chimes sound as the clock hands align at 12. The face or floor or something form a spiral staircase. Farin tells Link to go.
Link goes down the stairs to the chamber of the triforce. It hovers before him, shining and dramatic. So dramatic that there isn't even background music in here. The four cogs float away from Link and the shape of the Hero appears. He says "you won't be needing any of their magic anymore, I think you've proved that you're courageous enough to stand on your own. A true hero." He turns around and looks at the triforce. "Much bloodshed has come from coveting this, and if one who isn't pure gains it, more will follow. Maybe you've never wanted more than to take care of your friends. But it's a shadowy world, even I'm not sure who the bad guys are all the time. It's said that if a person with an upright heart touches the triforce, his heart's wishes for peace will be granted." He turns back around. "So are you one? What will you do?" The hero walks to stand beside Link and stare at the Triforce. The screen fades out.
Then we get one of those ALTTP sequences of all the world's conflicts being resolved (implying that either Link wished and had a righteous heart, or that he knew that people aren't all good or bad, including himself, and just trusted the good side of each person to work out their own issues. Magic or humanitarianism? Unresolved ending! Ambiguity!). The deku get their king worked out, anybody else in the forest is doing good, the Zora royalty displays their bravery, the gorons bite rocks, Link's gang is dressed nicely and hanging out with Zelda in the castle, etc.. Everywhere, there is more equity and teamwork. The motif of disparity is resolved.
At the end, the game comes back to Link in a rebuilt section of the slums, and the player regains control (although he can't save, or leave this section of the slums). There is a mix of rich and poor people helping each other out, businesses are flourishing, there are plants and flowers growing, an old fountain that never worked is running again, etc.. People and different races from outside Hyrule town have journeyed here, too. Link will be able to find one or two people he helped out from different portions of the game. Some people the player can talk to have information about how the other places in Hyrule are doing. The Sheikah left the fort destroyed so that the path to the desert is open. They and the Gerudo realized after their huge battle that nothing good could come of their animosity, and they started working together to rebuild a joint Shiekah/Gerudo city. The Gorons have started their industry up again and have plenty of other people/races helping them. The Zora prince and princess are adventuring all over Hyrule to learn about the different cultures and be better leaders. Etc.
Link walks through all of this to come to the gang's hideout, which too, is fixed up. Inside, there's a small bakery in their kitchen that's giving out bread and soup to people, there's a library where a couple people are learning about stuff to better themselves and understand other cultures, and everybody in the gang is contributing to the community.
Link walks up to Farin, who's hanging out with younger children, telling them a story. He concludes by saying: "...the brave hero knew that the enemy was dangerous, but when he thought of all his friends, and how he would help them all if he could defeat the dragon, he gained strength. He beat the dragon, and if ran away, never to scare the village again. The end!" ...and the kids run off. Farin walks up to Link and tells him, "I've never been much of a story teller. I've never had time between worring about my people or trying to stop Ganon to make up stories. But you know what? When I think of what you've done for everyone, selflessly helping out all of Hyrule, I get inspired. Link, I'm proud of you. You might have grown up a thief, and that's my fault. But you helped create a world where nobody has to steal anymore. You're a king among thieves."
THE END fades onto the screen, over a picture of Link and the gang waving goodbye to Farin as he walks a packed horse toward the desert.