In The Legend of Zelda: Spirit Tracks, a young Link travels to Hyrule Castle in order to become a qualified train engineer. At the ceremony, Princess Zelda presents him with a certificate as well as a secret note asking Link to meet her in private and warning him against trusting her chancellor, Cole. Link sneaks into Zelda's room and helps her to escape the castle. Recently, the magical Spirit Tracks around Hyrule had been disappearing mysteriously, and Zelda believes that an explanation can be found at the Tower of Spirits. However, while on their way there, more of the tracks vanish suddenly, causing Link to crash his train. In the distance, the Tower of Spirits breaks into sections, and the horrified duo (along with Link's former instructor, Alfonzo) are attacked by Chancellor Cole and his sidekick, Byrne. Cole and Byrne separate Zelda's soul from her body, spiriting the latter away.
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Despite the loss of her body, Zelda remains behind as a spirit. She travels with Link to the Tower of Spirits where they meet Anjean, a Lokomo (a guardian of the Spirit Tracks), who tells the two of them that the Spirit Tracks are disappearing because the demon king Malladus is slowly gaining the power to escape from his restraints. In order to stop him, Link and Zelda must restore four rail maps in the four farthest corners of the kingdom. After the fourth map is restored, Byrne is revealed to be a former Lokomo and the apprentice of Anjean who'd later defected and joined forces with Cole. When Link and Zelda return to the tower, they encounter Byrne and, at the top of the tower, Malladus' awakened spirit. He successfully possesses Zelda's body, then turns on Byrne before leaving with Cole on the Demon Train.
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After gathering special items with which to fight Malladus, Link battles the Demon Train, Cole, and Zelda's possessed body. Malladus leaves Zelda's body and possesses Cole instead, but Link is able to defeat this new entity with Zelda's help. With Malladus destroyed forever, Anjean, Byrne, and the other Lokomos ascend into the sky while Link and Zelda watch, hands intertwined.