As Link leaves the Tower of Hera, Sahasrahla contacts him to say that he’s ready to claim the Master Sword. The Master Sword is where the last Link left it, deep in the Lost Woods. When Link uses Irene’s bell, the broom shows up without a rider. That probably means Yuga’s caught Irene, but… Irene’s been prickly about the whole fast-travel arrangement, so it wouldn’t be too out of character for her not to come.
In the northwest corner of the Lost Woods, there’s a tricky section where Link needs to go the proper way to venture deeper into the woods. There are Poes in the area, and on the first screen, one shows him the way to go after dancing among its mates to confuse the player. On the next two screens, two and three of the Poes go in the way that Link isn’t supposed to go, so the player needs to keep track of the misleading Poes and go the way none of them does. After solving all three puzzles, Link comes to the clearing where the Master Sword sleeps again forever until Nintendo gets an idea for a sequel in the Downfall timeline. Using the pendants, Link draws the Sword from its pedestal, and Sahasrahla contacts him to say it can break the barrier on Hyrule Castle. When Link comes to the castle, Sahasrahla’s there, and he offers to save the game for Link after the barrier is dispelled.
As in A Link to the Past, the main dungeon now takes place in the central tower of the castle. Halfway through the dungeon, Link comes to find that, once again, he’s too late. Zelda and Yuga are confronting one another – Yuga says his acquisition tour is nearly complete, saying that Impa is the last of the seven sages he needed. Zelda asks what he intends to do with them, speculating that he intends to bring Ganon back. Yuga is completely uninterested in what she’s saying, and turns her into a painting as well. He recognizes Link from their earlier meetings and summons soldiers to fight him, while retreating higher up the tower. Link’s got a short gauntlet to get through before setting up a rematch.
Yuga is frustrated that Link refuses to do what he’s supposed to and go away. For this fight, he creates two duplicates and spreads them around the room; he and his duplicates electrify huge areas, so the only way to avoid damage is to find the real Yuga and attack him first so that area remains safe. After a while, the door Yuga was standing by at the start of the fight opens, and Yuga leaves with one final taunt that he does intend to release Ganon, at which point “lowly creatures like [Link] won’t be worth [his] time.” Link follows Yuga to another tower, where he finds a glowing gap in the wall behind a curtain. Link merges with the wall and goes through the gap.
Link is now in an alternate dimension; the Triforce in their crest points down instead of up. Link catches up to Yuga, finding him in a ritual that has him surrounded by the paintings of the Sages and Zelda [1]. (We get a look at the paintings, confirming that Gulley, Oren, and Irene are among the sages. The seventh isn’t seen as clearly, but appears to be Rosso.) He says his goal is to attain true beauty, then uses the sages in the ritual to summon and merge with Ganon. And, to be clear, we’re not talking the Gerudo form that may be good-looking if you’re into that sort of thing, but the pig demon form. Truly, this is the upside-down land.
Seriously, it seems what he’s really after is the Triforce of Power, suggesting he took Zelda to gain the Triforce of Wisdom. The Sages’ paintings scatter to the corners of the map, but Zelda’s remains in the castle. Ganon-Yuga (Yuga-Ganon? Yuganon?) roars, knocking Link over, and then he advances to strike, only to be thwarted by a woman appearing from a portal between them and binding him. The woman introduces herself as Princess Hilda, and welcomes him to her kingdom, Lorule. To stop Yuga, Link will need to awaken his full potential by rescuing the Sages. She sends him away on his quest.
Next: The dark world.
[1] Zelda was a Sage back in Ocarina of Time, and one of the seven descendants of the Sages/Wise Men in A Link to the Past. But apparently not anymore.