Cerebro detects that the technorganic alien race known as the Phalanx have returned and have contaminated a sentinel manufacturing facility. The plot is narrated through the Cerebro and Professor X's communication with each other. The game is based on the current story arc from the comics at the time of development. Players begin the game with eight lives (meaning nine attempts) that are shared by all characters, with no way to gain more.

In addition to these attack powers, each character has several lesser abilities, maneuvers and quirks which make gameplay a different experience with each (see above) these attack powers can be used to reach hidden health pickups (which take the form of a double helix) or as a shortcut. The attack powers increase in power when the character has nine or ten bars of health and can perform different functions if the character is in the air.

Some of the mutant attack powers can be charged to a greater effect by holding down the power button. Unlike the preceding game, there is no energy bar that limits the amount of mutant attack powers a player can use.

Įach character has a 'mutant attack power' that can be used in combat. The game begins with a cold open the first level begins as soon as the game is turned on with a random character (depending on the direction the player pressed on the controller's d-pad) after completing the first stage, the title screen and credits roll, and the player is given the option to switch characters.

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