Inspired by the book The Tracks Go On and On, which director Eiji Aonuma read with his son; The Legend of Zelda: Spirit Tracks (Zelda no Densetsu: Taichi no Kiteki in the Japanese) brings an Industrial era setting to the formerly medieval-themed Legend of Zelda series.
"My son loved this book. When he was four or five, this was the book he'd bring me every night before bed. 'Read it, dad, read it!' That's the story, it's a very simple one, but the pioneering spirit, the kids building the railroad... Something about it seemed as though it would fit with Zelda. But I didn't tell the staff about this book." -Eiji Aonuma
As the first continuous sequel to a Zelda game on the same console since Majora's Mask, Aonuma thought of this game in the same way as that game, creating a brand new game and story while using the same assets made for it's predecessor, in the same way Majora's used from Ocarina of Time. Spirit Tracks took two years to make, as opposed to Majora's Mask, which was developed for only one year.
As it is tradition to make a direct Zelda sequel to have gameplay elements completely different from their previous title, the team decided to use the Phantom enemy from Phantom Hourglass as a second playable character that can be controlled simultaneously with Link using the touch screen to add a new mechanic to solve puzzles, as well as for story purposes.
Sometime after the events of Phantom Hourglass, Link, Tetra, and their crew discovered a huge new land mass that they could colonize and call New Hyrule. The descendant of Tetra went on to become the new Princess Zelda, while the descendant of Link went on to become a train engineer for the Royal Railroads. The land was populated by the descendants of the inhabitants of the Great Sea.
Link learns from Zelda that train tracks have started to disappear from the railroad, which, as well as being used for transportation, were responsible for sealing an ancient evil force named Malladus. Together with Link's engineer teacher and former swordsman Alfonzo, the trio head out to investigate these disappearances, only to be ambushed by Cole, a demonic servant to Malladus posing as Zelda's chancellor, and a powerful warrior named Byrne (or Staven, depending on the localization) who seek to revive this ancient evil by stealing Zelda's body to use as a vessel for said force.
This leaves Zelda's spirit wondering around aimlessly, unseen by all whom she passes. All except for Link, anyway. Upon discovering this, Zelda enlists the help of the young engineer to help her regain her body and stop the resurrection of Malladus by restoring the Tower of Spirits.
In a departure from the previous two games in this thread of the Zelda universe, Link now gets around Hyrule via train instead of a boat.
Link's train, much like his predecessor's boat, sports a cannon to fend off any hostile creatures that get too close. Like any Zelda game, Spirit Tracks includes dungeons full of environment based puzzles, giant bosses, and all new items and weapons to help the player throughout the game.
New to this game is a player controllable Phantom Knight that can be used to safely traverse hostile terrain. Link can ride on this Phantom Knight to cross lakes of lava or use it to block fire in Link's path.
For the first time in a canon Zelda game, Zelda is a playable character aiding Link with her ability to control the Phantom Knights in the central Tower of Spirits. Like its predecessor, Spirit Tracks uses the touch screen for all of Link's actions. Movement is done by placing the stylus on the touch screen in the direction you wish to move in, thereby causing Link to start running (or walking if the player places the stylus close enough to Link's current position) in that direction.
For combat, the player simply make a quick swipe across the screen to use Link's sword. They can also just tap an enemy to attack them as well. Other actions, such as picking up and moving an object (like pots, bombs, or whatever else Link can grab) simply require the player to tap on that object to pick it up, and tap again where they wish to put or throw said object.
The game uses the DS microphone frequently, specifically for the Spirit Flute and the Whirlwind.
- Princess Zelda - The descendant of Tetra and ruler of Hyrule.
- Link - The protagonist of the game whose latest incarnation sees him as a train conductor.
- Niko - A surviving member of Tetra's original pirate gang, he is now over 100 years old and narrates the game's prologue.
- Alfonzo - Link's mentor in the Royal Railway. He is a great swordsman and train engineer. A descendant of the original pirates.
- The Postman - A traveling postman in charge of delivering letters across the kingdom.
- Chancellor Cole - Zelda's suspicious chancellor whose interests may lie outside of the royal family.
- Anjean - A member of the Lokomo tribe and the guardian of the Tower of Spirits. All the Lokomo have train-related names, and ride around on little wheeled carts.
- Byrne - A very powerful companion of Chancellor Cole, who joined up with him for his own reasons. He was once of the Lokomo and was formerly Anjean's apprentice.
- Gage - The Lokomo of the Forest Realm.
- Steem - The Lokomo of the Snow Realm.
- Carben - The Lokomo of the Ocean Realm.
- Embrose - The Lokomo of the Fire Realm.
- Rael - The Lokomo of the Sand Realm.
- Honcho - The head of the walrus-like Anouki tribe of the Snow Realm. The other Anouki are Bulu, Kofu, Noko, Yefu and Yeko.
- Kagoron - The strongest warrior of the Fire Realm's Goron tribe. He helps Link by providing him with the train's wagon, necessary for several quests involving moving cargo.
- Ferrus - A train-obsessed traveler and photographer who Link meets several times. He indirectly teaches the player how to observe the laws of the rails when carrying passengers.
- Beedle - A descendant of the Wind Waker merchant who, like his Skyward Sword counterpart, flies around in a store connected to a hot air balloon. As with previous games in which he appears, he provides membership tiers and bonus for frequent buyers.
- Rabbitland Rescue Man - An odd man obsessed with rabbits who has built a safe haven for them. Link can capture rabbits while he travels around by train, and return them to the sanctuary for prizes.
- Linebeck III - The grandson of Phantom Hourglass's roguish corsair Linebeck, who runs a trading post between the Forest Realm and the Ocean Realm. He is every bit as treasure-obsessed as his ancestor. He also looks identical, but for a straw boater hat.
- Stagnox - The Armored Stag Beetle of the Forest Temple. Resembles a giant stag beetle.
- Fraaz - Master of Icy Fire of the Snow Temple. Resembles a miniblin, but wielding magic similar to Twinrova's.
- Phytops - Barbed Menace of the Ocean Temple. A large kraken type creature with spiky, vine-like tendrils.
- Cragma - Lava Lord of the Fire Temple. A cyclops/rock golem type creature.
- Byrne - Chancellor Cole's minion. Fights using his speed and retractable claw.
- Skeldritch - Ancient Demon of the Sand Temple. An immense, skeletal sandworm creature.
- Demon Train - The Demon King's diabolical train.
- Chancellor Cole - Zelda's chancellor who seeks to summon the Demon King. Cannot be attacked directly, but needs to be chased away before the player can reach Malladus during the fight on top of the Demon Train.
- Malladus - The Demon King. Has several forms, including Princess Zelda's at one point.
- Dark Link - An optional boss found at the end of the hardest level of Take 'Em All On, a Survival Mode style combat mini-game. He is able to use Link's bombs and arrows in addition to his sword.
- Aboda Village
- Hyrule Castle Town
- Trading Station
- Rabbitland Rescue
- Forest Sanctuary
- Forest Temple
- Snow Sanctuary
- Snow Temple
- Anouki Village
- Wellspring Station
- Bridge Builder's House
- Slippery Station
- Snowdrift Station
- Ocean Sanctuary
- Ocean Temple
- Papuchia Village
- Pirate Hideout
- Lost at Sea Station
- Fire Sanctuary
- Fire Temple
- Goron Village
- Goron Target Range
- Ends of the Earth Station
- Disorientation Station
- Dark Ore Mine
- Sand Sanctuary
- Sand Temple
- Tower of Spirits
- Beedle's Air Shop
Like its predecessor, Spirit Tracks features a multiplayer mode that similar to Pac-Man where up to four players can compete to collect as many force gems as possible, while avoiding Phantom Knights, before time runs out. The mode features six maps, each with their own traps and hazards, which are somewhat based on the various temples from the story.
The mode does not support online, but does support download play.