This part will take us up to the final boss fight.
After the Demon Train has stopped, we will be asked to save our game, which we might as well do. In the passenger car of the Spirit Train, Anjean tells Link and Zelda now is the time to fight Malladus, and that she will accompany them. Byrne offers to go in Anjean's place, but Zelda realizes they are both injured and tells them that they need to stay behind and let herself and Link take care of Malladus. Anjean concedes to Zelda's judgment and causes Phantom armor to appear so that she will be able to help Link. Zelda thanks Anjean for her help and tells Link it's time to go. However, before they head off, Zelda asks Link what he will become when the whole thing is all over and they resume their normal lives. Whatever the player answers from the three choices given (Engineer, Warrior, or Dunno), Zelda will understand without judging Link. (It will, however, affect the ending of the game, as shown below.) Anjean watches as Link and Zelda depart, saying that her ancestors would be proud of the princess, while Byrne broods silently.
Cole and Possessed Zelda
Link and Zelda climb on top of the Demon Train, where Chancellor Cole appears at the front. Zelda tells Cole that this is where it ends, but Cole says it's time for them to receive their punishment. He causes the Demon Train to start up again, then calls upon his lord Malladus to destroy the heroes. Malladus now has more control over Zelda's body as he stands at the front of the Demon Train, waiting for Link and Zelda to approach him.
Our goal is to help get Zelda to the front of the train where Malladus in Zelda's body is and then strike him with a Light Arrow when he is in Zelda's grasp in her Phantom form. Direct Zelda to move forward toward the front of the train. Along the way at the start, Cole will cause phantom mice to circle around and close in on Zelda, shocking her until he is able to manipulate her with puppet strings. Slay the phantom mice before they get close to Zelda, then get her to continue moving forward. If one of the mice gets a hold of Zelda, quickly back away from her and use the Boomerang to snip the puppet strings. Continue to stay close to Zelda as she gets closer to Malladus. As she does, Malladus will now fire an energy beam in Zelda's direction, and also the platforms will begin to shift left and right. The energy beam has no effect on Zelda, but it can hurt Link. Have Link avoid the energy beam as he continues to protect and guide Zelda to the front of the train, slaying the phantom mice Cole continues to create.
When Zelda finally grabs hold of Malladus in her body, time a Light Arrow shot so that it strikes Zelda's body. You only have a limited amount of arrows to do this, so make sure you're fully stocked.
Final Boss: Malladus
With Zelda's body struck with the Light Arrow, the Demon Train falls out of the sky and crashes to the ground, and Malladus is forced out of her body. Zelda's spirit tries to reinhabit her own body but fails. Malladus tries to reinhabit Zelda's body, but is held off by Byrne, who tells Zelda to concentrate on reclaiming it. As she does, Zelda now falls out of the sky and is caught by Link, happy to be back in her own body. But it isn't over for Malladus yet. He first destroys Byrne, then much to Chancellor Cole's horror, he consumes his underling's form and possesses it, transforming it into a giant blue warthog-type creature with ram horns. Though Malladus feels his spirit starting to slip away from this form, he will use it in the time he has left to make the world crumble. Zelda realizes it is time to take down Malladus once and for all.
In the first part of the battle, we need to protect Zelda as she concentrates on charging herself with the power of the spirits to help Link in the latter part. Malladus will hurl fireballs from his mouth at Zelda, which we need to strike down before they touch Zelda, causing her charging power to dissipate and costing Link some heart (meter) damage. At some points during the attack, Malladus will hurl four fireballs at once in four different directions. We need to quickly strike them down from all four sides. Once Zelda is fully charged, she will lead us in the final Lokomo Song that we need to play as a duet. This will cause the other Sages to appear playing their instruments as they lend their power to defeating Malladus. This will also make a bright-shining target appear on Malladus' back for Zelda to use the Light Arrows to strike.
Now begins the next part of the battle: Link must distract Malladus so that Zelda can strike the target on his back with Light Arrows. During this part, the upper screen will depict Zelda's point-of-view while the bottom screen depicts Link in action with Malladus. To attract the evil one's attention, keep swiping at his two front legs, but beware of his paw swipes and horn gashes; also, if Malladus hurts Zelda, Link also takes damage. When the cursor that appears on Malladus' back turns yellow and Zelda has a clear shot, tap the arrow at the bottom of the lower screen to launch a Light Arrow. After the third hit, he will fall down so that Link can strike at his head, breaking off one of his horns. However, Malladus will soon get up and breathe out some fireballs at you. Repeat the same process so you can knock off the beast's other horn. When Malladus goes down for the third time, strike his head with the sword, then keep quickly rubbing the stylus back and forth so Link can jam the sword into Malladus' forehead crystal. Zelda will also come in to give Link a hand in forcing the sword inward. Soon the crystal will break, and Malladus will cry in anguish as light from within causes his possessed body to explode.
Success!!! You've just beaten the final boss of the game.
After Malladus' possessed body disintegrates, Anjean joins Link and Zelda, telling the princess not to regret not being able to save Byrne, because her people, the Lokomos, don't disappear that easily. She causes Byrne's spirit to appear in a light form, telling the princess that he may not have any memory of these events, but years from now he will return in a new form. She tells the two heroes that Lokomos weren't meant to just protect the Spirit Tracks, but also they were meant to watch over mankind. Believing that her job is now done, Anjean ascends from her motorized wheelchair into the sky and, after telling Zelda to watch over the land and Link to watch over her, changes into a light form before departing into the heavens with all the other Lokomos. Link and Zelda hold hands as they see the Lokomos disappearing into the sky, realizing the future is now in their hands.
This is the ending you get when you select Engineer:
After the credits have rolled, Princess Zelda is back in her chambers in Castle Town as the reigning monarch of New Hyrule under the watchful guidance of Teacher. She is looking at a picture of herself and Link together on their adventure, possibly taken by Ferrus, as she is signing papers. Then she hears a train whistle outside her window. She goes over to the window and waves as she watches Link (unseen on camera) manning the Spirit Train on the restored Spirit Tracks of New Hyrule, happy that he is serving her as the royal engineer.
This is the ending you get when you select Warrior:
After the credits have rolled, Princess Zelda is back in her chambers in Castle Town as the reigning monarch of New Hyrule under the watchful guidance of Teacher. She is looking at a picture of herself and Link together on their adventure, possibly taken by Ferrus, as she is signing papers. Then she hears swordplay outside her window. She goes over to the window and waves as she watches Link (unseen on camera) training with the guards, happy that he will one day serve her as a full-fledged warrior.
This is the ending you get when you select Dunno:
After the credits have rolled, Princess Zelda is back in her chambers in Castle Town as the reigning monarch of New Hyrule under the watchful guidance of Teacher. She is looking at a picture of herself and Link together on their adventure, possibly taken by Ferrus, as she is signing papers. Then she turns toward the window, as if she is either expecting to hear something or just wondering what Link is doing with his life now. She smiles as she returns to her signing of papers, before the camera pans out through the window and turns toward the sky.
And so the story ends.