Link wakes up in a bed in the castle, with Zelda’s mentor, Teacher, watching over him and Alfonzo. Alfonzo’s hurt and says taking care of Zelda is now up to Link. Teacher’s been wondering what the hubbub is all about. Link tries to explain it to him, but when he realizes that Link’s saying Zelda’s been kidnapped, his first instinct is to run and tell Zelda. So he’s useless. As Link leaves the room where he was recovering, he sees the ball of light that flew out of Zelda – it’s Zelda’s spirit, who’s trying to get the guards to help her but they can’t see her. Link follows her to her bedroom.
Having someone who can see her lifts Zelda’s mood a little, and she goes from apologizing to Link for getting him hurt, to wondering how she never realized Cole was evil, to talking to herself wondering what’s going on. She decides she still needs to get back to the Tower of Spirits, and asks Link to take the Spirit Flute, the pan pipes she was playing earlier. There’s one more thing – with the Spirit Tracks gone and Alfonzo’s train wrecked, they have to go to the Tower of Spirits on foot. And, of course, the way is filled with monsters, and the guard won’t let Link out without a sword. Link asks the guard captain for a sword, which comes with a tutorial on how to use it for people who didn’t play Phantom Hourglass. (Fortunately, the actual directions are skippable.) Link can also return to the shop in town to buy a shield.
Immediately outside the back exit of the castle, Link finds a field overrun with new enemies, evil nuts called Spinuts. There’s a guard out here who’s having trouble keeping them at bay, and he points to where the tunnel used to be before it got caved in. But, of course, when God closes a door, he gives Link a bomb to blow it back open. The tunnel is a basic dungeoneering tutorial: returning enemies (Keese and ChuChus), switches, blocks, keys and locked doors, and a simple puzzle. There’s one last bit of fun, revealing that Zelda is terrified of rats.
Inside the Tower of Spirits, Link and Zelda find a train, and finally meet the sage of the tower, Anjean. Anjean pokes fun at Zelda’s ghostly state, before revealing that she was friends with one of her ancestors – probably Tetra, from the way she’s talking. She moves on to talking about more pressing matters: Cole’s actions have weakened the seals on the Demon King, Malladus. She’s doing what she can to hold him back, but it’s a losing fight. The other big revelation is that Cole will need a suitable host for Malladus’ spirit: Zelda’s body. Hearing this, Zelda flips the pancake out.
Anjean lays out the quest: Zelda’s body and Malladus’ spirit are at the top of the tower. To get there, stop the release, and recover Zelda’s body, the spirit tracks need to be restored by recovering maps to the four temples and clearing them out. So, Zelda goes to Link, telling him to get on with it. “I will wait for you here. That’s what princesses have always done. From what I understand, it’s kind of a family tradition.” It’s a funny scene, even without Zelda’s mocking her predecessors, because of how frantic Zelda is throughout it all (and Link’s expression, once we see his face after Zelda’s tirade). But, as it turns out, she won’t be sitting on the sidelines this time: Link can’t make it through the tower alone, Anjean’s using all her power to hold back Malladus, Alfonzo is injured, and bringing someone else in is going to take too long. So… Zelda’s going to be Link’s companion for this adventure. That’s awesome, and it’s about damned time.
The Tower of Spirits is clearly the successor to the Temple of the Ocean King. It’s a central location with the maps to the dungeons, it has Phantoms and safe zones. There are some key differences: It’s not timed (so the Phantoms will presumably try to kill Link directly, rather than draining his time), and Anjean explains that Link can power up his sword with Tears of Light to fight back against the Phantoms a little. However, when he tries it, it only stuns the Phantom for a little bit; the Phantom recovers and attacks, but the attack is stopped short when Zelda gets close to the Phantom and displaces the spirit inside, possessing it herself.
Phantom Zelda has purple highlights on her armor, the Triforce crest on the back, and glowing pink eyes. She’s not thrilled about being in the Phantom, but realizes it can be useful, and strikes a heroic pose before the two of them continue up the tower. The rest of the tower is learning to control Link and Phantom Zelda in tandem – it works like when Link was sneaking Zelda out of the castle. Only now, it’s Link who has to remain out of sight while Zelda can distract the Phantoms. She can kill enemies with her sword, hit switches, and walk over spikes… but she’s still terrified of rats, so Link has to kill them.
On the third floor, Zelda is driven out of the Phantom, and Link’s sword loses its power. The two find the first rail map, causing some of the Spirit Tracks to reappear. That’s as far as they’ll get right now, so they return to the tower lobby. Anjean points out the temple on the map, but the Tracks don’t reach it yet. She tells Link and Zelda to look for her people, the Lokomos, starting with the forest sage, Gage. By playing the Lokomos’ sacred instruments – including the Spirit Flute – they’ll be able to restore the tracks and visit the temples. She also lets them take the Spirit Train, so they hop aboard and head off.
Next: Link gets an item to blow gas away from a bug's butt.