The Legend of Zelda: Spirit Tracks :: Boss GuideStagnox, Armored Colossus
Right from the start of the fight, keep your distance away from Stagnox and run around him. Stagnox will turn and attack slowly. Dodge the attack and use the whirlwind weapon to send a gust at the purple fog near his back to move the fog and stun Stagnox. When he is stunned, attack his back.
Repeat this a few times and eventually Stagnox will fly up in the air and send enemies for you to fight. Hit the enemiees to turn them into spiked balls. When Stagnox comes in for an attack, stand behind a spiked ball and whirlwind it at Stagnox. This will stun him and you can attack his back again until he is defeated.
Fraaz, Master of Icy Fire
After awhile, Fraaz will split up. If you hit one of the mini-Fraaz with the boomerang, you can see if it is fire or ice and then use the boomerang through the torches again. If Fraaz destroys the torches, wait until it shoots out fireballs and use the fire on the ground against him when he switches between fire and ice.
Phytops, Barbed Menace
Use the whip on Phytops's vines and pull out a spike. Then target the front of Phytops and shoot the spikes at him to break his purple shield. When his eye is completely visible you can shoot a spike at the eye to stun him. When he is stunned, run up and hit his eye with your sword. Repeat this until Phytops is defeated.
Cragma, Lava Lord
Use your bow and arrow to hit Cragma in the stomach. If Cragma smashes the ground and makes a big rock appear, stand near the rock and dodge Cragma's at the last second to make him hit it. This will make a platform that you can pick up and take to the small lava pit and use to reach the moving cart on the right side of the room.
Ride on the cart with your bow and arrow out and shoot at Cragma's body whenever you can see it. You will only deal damage if Cragma is shiny. Eventually you will be able to shoot Cragma in the eye, which will make him fall down and you can run up to him and hit him with your sword.
Wait until Byrne tries to hit you with its gauntlet. Dodge him and send the Zelda phantom at him. Zelda will pull Byrne down and you can hit him with your sword. When Bryne stops jumping you can just keep hitting him with your sword to get through his blocks. If he charges at you, hide behind Zelda and the phantom will hold Byrne down, allowing you to hit him some more.
Skeldritch, Ancient Demon
Use the sand wand to keep the rocks that Skeldritch shoots at you near by. You can then load the rocks into the catapult and fire at Skeldritch. Skeldritch's weak spots will change around, so load the catapult and move around so that Skeldritch faces the right way and use the bow and arrow to activate the catapult.
The Demon Train
First shoot the explosive barrels that appear out of the rear car. Eventually you will destroy the rear car and will have to deal with the laser cannons. After you shoot and destroy all the laser cannons, you will need to shoot the rotating lasers to stun the Demon Train. When it is stunned, you can then ride in front of the train and shoot its face.
Puppet Zelda and Cole
March the phantom towards Puppet Zelda, stay behind the phantom to avoid the lasers. As you progress, you will need to kill all the rats that Cole sends at you. If he starts controlling the phantom, use the boomerang to cut the puppet strings. Pick up Zelda and go to the very edge of the train. Shoot Puppet Zelda with a light arrow to move on.
Malladus, Demon King
Run around with Link and hit Malladus to distract him. When Zelda is ready, tap the arrow on the bottom of the screen to launch a light arrow. After three light arrow hits, you can hit Malladus with your sword. Repeat this three times to defeated Malladus.