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After learning of Chancellor Cole's plan to revive Malladus, the Demon King, Link is given the task of restoring the Spirit Tracks and stopping Chancellor Cole. After restoring part of the Spirit Tracks by obtaining part of the Rail Map from the Tower of Spirits, Link is instructed to travel to the Forest Sanctuary and meet Gage, one of the Lokomos. The inhabitants of the lumber town Whittleton aid Link in traversing the Lost Woods and finding the Forest Sanctuary. At the Forest Sanctuary, Link learns the Song of Awakening on the Spirit Flute. Gage and Link play a musical duet, opening the way to the Forest Temple. After the defeat of Stagnox, the Spirit Tracks in the Forest Realm are restored, and Link returns to the Tower of Spirits to retrieve another part of the Rail Map.
The Forest Temple is full of weak enemies and purple smoke that inflicts 1/4 damage to Link's health; Link needs to use the Whirlwind to blow the smoke away. He can also find a Stamp Station there. Puzzles include blowing a Small Key off of a ledge to a place where Link can pick it up.
|Anjean · Byrne · Chancellor Cole · Link · Malladus · Princess Zelda|
—Full list of characters
|Stagnox · Fraaz · Phytops · Cragma · Byrne · Skeldritch · Demon Train · Chancellor Cole · Malladus|
| Fire Realm · Forest Realm · Ocean Realm · Sand Realm · Snow Realm|
—Full list of locations
|Forest Temple · Snow Temple · Ocean Temple · Fire Temple · Sand Temple · Tower of Spirits|
|Lokomo Sword · Rail Map · Recruit's Sword · Recruit Uniform · Spirit Flute · Spirit Tracks · Spirit Train · Stamp Book · Tears of Light|
|Boomerang · Whip · Whirlwind · Bow · Sand Wand · Bow of Light|
|Anouki · Demon · Goron · Hylian · Lokomo|