Each level has waves of enemies plus a mutant boss who all must be defeated to progress to the next stage. X-Men: Reign of Apocalypse is a side-scrolling action beat 'em up with 12 distinct levels. Other X-Men from the 616 Marvel Universe, such as Colossus and Nightcrawler, are allies of Apocalypse in this alternate universe and must be defeated. Boss enemies include classic villains from the comics such as Blob and Magneto. Each character has a different super power that gives them a unique playstyle. The playable X-Men roster consists of Wolverine, Cyclops, Storm, and Rogue. The X-Mansion, the Blackbird, Genosha and other familiar locations are present in the game. The setting takes place in an alternate universe controlled by Apocalypse, with backgrounds that stay true to the X-Men comics. The X-Men must battle their way through Apocalypse's army of Sentinels and Mutants in order to return to their universe.
They soon discover that they are in an alternate universe under the control of the evil mutant, Apocalypse. Returning from their journey in the Mojoverse, the X-Men return to the destroyed remains of their home, the X-Mansion.