- "Ah, I'd completely forgotten that today was the graduation ceremony. Huh, I didn't know they gave engineer certificates to little kids like you... I guess times are-a-changing."
- — Hyrulean Soldier
The game opens up with Link traveling to Hyrule Castle to attend the Graduation Ceremony, where the honor of Royal Engineer will be bestowed onto him by Princess Zelda herself. Once there, he finds that many Hyrulean Soldiers and others have been eagerly awaiting his arrival, while others have completely forgotten about the ceremony.
As Princess Zelda rewards Link for his service, she slips him a note, warning of the suspicious Chancellor Cole, and to take a hidden path and meet her in secret. This in turn spirals into the overall story arc of Spirit Tracks.
Events in The Legend of Zelda series
|Age of Burning Fields · Creation of Hyrule · Great Calamity · Great Cataclysm · Great Flood · Peace Agreement · Shipwreck · Slumber of Restoration|
|Great War of Ikana · Hyrulean Civil War · Imprisoning War · War of the Bound Chest|
|Carnival of Time · Champion Festival · Hyrule Festival · Korok Ceremony · Picori Festival · Picori Festival Tournament · Wing Ceremony|
|Autumn · Spring · Summer · Winter|
|Blood Moon · Endless Day · Endless Night · Graduation Ceremony · Horde Battle · Jam Session · Lunar Phases · Oasis Flight · Restoration Ceremony|
|Bad Uncle Rupee's Ashen Rupeeland · Destruction of Termina · Game Over|
|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|