At the start of the fight, Stagnox will be on the ground and will try to ram Link with its horn. He must run to its backside and use the Whirlwind to remove the gas which will allow him to attack its vulnerable backside. Eventually it will take flight and release Blastworms, creatures that revert to bombs when attacked. Link must hit them with his sword without detonating them and use the Whirlwind item to blow one of the Blastworms at Stagnox when it charges at him to flip the boss over, to once again leave itself vulnerable to attack.
Stagnox's name is derived from "stag," as in a stag beetle, upon which it is based. The "nox"-part may be derived from noxious, meaning toxic, which may refer to the poison gas Stagnox's rear end is emitting.
Stagnox is the only boss in the game that appears four times.
Stagnox was the first boss revealed for Spirit Tracks, appearing in the first trailer.