The Street Fighter characters uses their Street Fighter Alpha 2 forms and their moves were given upgrades to match the larger-than-life atmosphere of the Marvel games for example, Ryu's Hadouken is much larger than it is in other games. The X-Men characters come largely unchanged from X-Men: Children of the Atom and Marvel Super Heroes, with the exception of Rogue, Gambit, and Sabretooth, who are new to the series. Also, the 'Variable Combination' is a two-character Hyper Combo (the super moves featured in the game) which costs two levels, and will switch the player's current character as long as neither character gets hit during their Hyper Combos. There are other ways to bring the character's partner in the 'Variable Counter', which replaces the Infinity Counter of Marvel Super Heroes, breaks the player's guard to bring the teammate in with a counterattack at the cost of a level of super meter. A match is over when both members of a team are defeated. If one character loses all of their vitality, then the tag partner will automatically come to play. The dormant character will able to recover a portion of their vitality, while the current character is fighting. During their taunt, they are vulnerable to counterattack. The starting character can tag the waiting one in at any time by hitting the Hard Punch and Hard Kick buttons, which activates the 'Variable Attack' the tag partner will jump in with an attack and taunt briefly. The player controls one character at a time, while the other awaits off-screen. Instead of the usual best-two-out-of-three round format, the game's matches consist of two-on-two battles between tag teams.

Street Fighter uses a system similar to the style developed in Marvel Super Heroes, and adds the tag team gameplay feature.

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