Wolverine is mysteriously contacted by an unknown party claiming to have information regarding his past. Deciding to follow this lead, Wolverine travels to Canada, and then Japan, battling against the Destroyer Program, Tri-Fusion, and Lady Deathstrike. Deathstrike informs Wolverine that he has been tricked and lured out, as Shinobi Shaw has placed a contract on his life. Believing that Shaw is hiding out in the Inner Circle’s base in Tokyo, Wolverine heads to track him down, battling Geist’s forces and Bloodscream along the way.
Cyber attempts to kill Wolverine by trapping him in a hallucinogenic nightmare, but Wolverine frees himself by turning Cyber’s toxin against him. Making his way to the Inner Circle’s mansion, Wolverine battles against Selene and Fugue, while Shaw flees. Falling into the catacombs below the mansion, Wolverine fights Fugue for a second time, defeating her, and makes his way deeper. At the bottom of the catacombs, Wolverine discovers the true mastermind behind the contract against him–the Great Beast, leader of The Hand.
Ultimately, Wolverine destroys the Beast, and returns to X-Mansion, where the X-Men greet him. Both versions are action/adventure platformers, and the player guides through large multi-floored levels, attacking enemies or solving puzzles to give him access to new areas. The Super NES version requires a set number of enemies to be destroyed before entry to the next area is granted. Both versions have a time limit that expires if the player takes too long.
Whereupon the character Elsie-Dee automatically finds Wolverine and kills him, wasting one of his five lives (Genesis version) or giving the player a game over (Super NES version). Both games feature a password function that enables the player to continue the game at any level. Both games give Wolverine a percentage of his available health, always starting at 100%. Upon taking damage, his energy will recover over time thanks to his mutant healing factor.