Synopsis
Spirit Tracks takes place approximately 100 years after the events of Phantom Hourglass. An incarnation of the protagonist Link, an engineering apprentice ready to become a qualified train engineer, travels to Hyrule Castle to receive his engineer's certificate from Princess Zelda. Though Zelda's adviser, Chancellor Cole, believes the ceremony to be completely pointless, as the Spirit Tracks that make up the train systems around Hyrule are slowly disappearing and rendering trains useless, Zelda continues with the ceremony. Once the ceremony is finished, Zelda secretly gives Link a note to meet her in her quarters later and a warning to not trust Cole. There, Zelda implores Link to help her escape the castle and take her to the Tower of Spirits with his train, where she believes the mystery of the disappearing tracks can be solved. To sneak out of the castle, Zelda gives Link the Recruit Uniform (with the same exact design as the Hero's Clothes from The Wind Waker and Phantom Hourglass) of the castle guards to blend in, distracting them while Zelda sneaks past.
While en route to the Tower of Spirits with Link's engineering teacher and former soldier Alfonzo, the tracks they are on disappear, nearly causing the train to tip over. As Link and Zelda watch, the Tower breaks into pieces, hovering above one another. They are ambushed by Cole, revealing himself to be a two-horned demon, and a mercenary named Byrne. Alfonzo and Link are unable to protect Zelda from Byrne's power, and Cole uses dark magic to sever Zelda's soul from her body. Cole and Byrne then take her body and depart, leaving Link unconscious.
Link later wakes up back in Hyrule Castle, with both he and Alfonzo having been found and rescued. After leaving the room, Link sees Zelda's spirit floating into the castle and goes after her. After trying to call on the castle guards for help, who, like everyone else, are unable to see her, she floats to her chambers. Not knowing that Link has followed from behind, the two finally see each other. Zelda tells him they must go to the Tower through a dangerous underground passage after retrieving the Spirit Flute, a magical pan flute that has been passed down from generations of the royal family, from her quarters before leaving. When they arrive at the lobby of the Tower of Spirits, they are met by Anjean, a Lokomo (a servant of the Spirits of Good) who is the previous owner of the Spirit Flute (Anjean gave it to Zelda's ancestors to help protect the kingdom), and can see Zelda's spirit form. She explains that many years ago, the Spirits fought the evil Demon King Malladus, and in the end, he was imprisoned deep beneath the earth. The Tower of Spirits and the Spirit Tracks that connect to it were built to contain Malladus, but with their disappearance due to Cole's involvement, Malladus will soon be able to escape, using Zelda's stolen body (containing the dormant power of the Spirits) as his vessel. Zelda then demands to know how to prevent the Demon King's return, to which Anjean replies that the Spirit Tracks have to be restored by retrieving and completing several ancient rail maps (one for each of the four realms of Hyrule) from the above floors of the Tower to restore the Spirit Tracks. Then, the Tower must be linked up by the Spirit Tracks to four different temples, one in each of the four known realms. When Zelda tells Link to get moving while she waited in the tower lobby, Anjean tells then that "ascending the tower alone is impossible," meaning that Zelda will have to accompany Link. She reluctantly agrees after the Lokomo reminds her that "this kingdom is your responsibility." After saving Link from a Phantom (a Tower guardian), she realizes that by collecting three Tears of Light and then having Link attack the Phantom from behind, she can possess the Phantoms to help Link within the Tower.
With the help of Zelda and the other Lokomos, Link restores the Spirit Tracks and most of the Tower of Spirits. After obtaining the final rail map, Byrne shows up to kill Link. Anjean shows up as well, revealing that Byrne is also a Lokomo that went rogue at a young age. This information shocks Link and Zelda, and Anjean teleports the duo down to the lobby before having an apparent battle with her former apprentice: Byrne. After restoring the Tower of Spirits and the Spirit Tracks to normal, Link and Zelda go back to the tower, There, they are blocked by Byrne, who had apparently beaten Anjean. The two overpower him and reach the top of the tower, where both Malladus's spirit and Zelda's body are located. Malladus successfully enters the vessel, and, knowing that Byrne was a servant of the spirits, attacks (and almost kills) him when he asks for the great power he hoped Malladus would grant him. It is shown that he is not yet used to his new vessel, and leaves with Cole on a Demon Train.
Anjean (and a now-reformed Byrne) then directs the two to find two artifacts they will need to find and defeat Cole and Malladus: the Compass of Light and Bow of Light. After retrieving both, Anjean gives Link the Lokomo Sword and joins Link and Zelda as they head for the Dark Realm where Cole and Malladus await. In the Dark Realm, Link battles the Demon Train, Cole and Malladus, securing Zelda's body and destroying the Demon Train. As Zelda prepares to rejoin her spirit to her body, Malladus attempts to possess her body again, but Byrne interferes and lets Zelda rejoin her body. Malladus instead destroys Byrne. Without a vessel, Malladus takes over Cole against his will, completing his resurrection. However, Cole's body is unable to contain Malladus' spirit for long, though he vows to destroy the world before he is completely rejected. Once again, Link and the restored Zelda work together to defeat Malladus with Zelda's magic, the Bow of Light and the Lokomo Sword, destroying the entity along with Cole forever.
After the battle, Anjean reveals that she and the other Lokomos are now leaving the kingdom, their duty to protect it from Malladus now complete. Anjean also reveals that Byrne is not dead, but only a newborn spirit which will be restored many years from now.
Anjean, Byrne's spirit and the other Lokomos then ascend into the heavens, as Link and Zelda watch, holding each other's hands.
Read more about this topic: The Legend Of Zelda: Spirit Tracks