The X-Men have come looking for their allies Storm and Forge, only to run into Freedom Force, who've been sent to capture them. Soon both teams find themselves caught in a bizarre time warp caused by the powerful being known as the Adversary, who has imprisoned Storm and Forge. Uatu the Watcher appears at the beginning and introduces the game as a parallel universe's version of the story from the "real" Marvel timeline in the vein of Marvel's What If? series. In this case, "What if a different team of heroes fought the Adversary?" To answer this question, the player forms a team of heroes from a choice of 15 past and present X-Men.
The game uses an overhead view during normal play as characters move around the map, as they look for enemies, health crates, and traps. When the X-Men encounter an enemy, the game switches to a side view close-up during the battle scenes. In each level the object is to search for a pair of Freedom Force members and defeat them in battle, but only the defeat of one villain will send the player's team to the next level. After completing enough levels the heroes are thrust into battle with the Adversary himself.
This Video Game contains examples of:
- Alternate Universe: The hook of the game, of course. Also how the Watcher explains things if the player loses, dooming the planet, and wants to play again.
- Arbitrary Headcount Limit: You can have five characters in your team, even though the X-Men roster that actually featured in the "Fall of the Mutants" storyline had seven note .
- Big Bad: The Adversary.
- Color-Coded for Your Convenience: The healing items come in different colors. Some characters can use some colors and not other colors. The only way to find out is to run into the item, ruining it if they can't use it or don't need it, and take notes.
- Cool, but Inefficient: The more effective an X-Man's attacks are the more energy they use. For instance Phoenix can kill most enemies from the other side of the screen just by using her primary attack one or two times, never mind having to aim. She depletes her energy bar faster than any other playable character, though.
- Eldritch Abomination: The Adversary.
- The End of the World as We Know It: If the X-Men all die the Earth crumbles away to nothing over the Watcher's shoulder.
- In-Universe Game Clock: The game operates on a day-night cycle, where at night you'll have a much smaller field of vision making it easier to bump into a trap or enemy without seeing it.
- Healing Factor: The game incorporates Wolverine's healing power; he's the only playable character whose health goes up along with his stamina when the team camps.
- Lazy Backup: In a fashion, since the individual X-Men are attacked by groups of enemies depending on how many enemies are in the group. That is, if you fight a group of two dinosaurs and a caveman, the first three X-Men in your line-up will have to win a fight before you can move on, but the last two party members will just stand around doing nothing the whole fight. You can of course switch those members to the front when wounds start piling up on the front-line fighters to keep going longer, though.
- Mana Meter: One of the games that has a second energy bar that's depleted by using their special powers, whether it's fighting enemies or clearing obstacles in the overworld.
- Names to Run Away from Really Fast: The Adversary may not sound like much...until you fight him.
- One-Winged Angel: The game goes straight past the Adversary's Indian shaman form he started with in the comics to his shadowy demonic form for his boss fight.
- Resting Recovery: Pushing C sets up camp and the heroes get their energy back (but don't heal, except for Wolverine) as they rest. You can be ambushed by wandering enemies while doing this if you aren't careful though.
- Series Continuity Error: The game shows Marvel Girl's X-Factor costume as red and yellow. It was green and yellow.
- Timed Mission: You have seven in-game days to find and defeat the Freedom Force member who arbitrarily unlocks the next level.
- Trickster God: The Adversary, but an unusually malicious one.
- Violence Is the Only Option: In the comics this game was based on the X-Men and Freedom Force called a truce because of the interdimensional catastrophe going on (the recap of the comic in the manual even makes this clear). Despite the game being built on the premise of seeing how things were different in alternate universes, the X-Men have no choice but to hunt down and defeat the Freedom Force members to unlock further levels. Teaming up in the face of an obviously much bigger crisis just isn't a possibility the game offers.
- A Winner Is You: After defeating all the villains, temporally-displaced monsters and then the demonic god behind it all in single combat, you get an extremely quick ending sequence. Then you're given a minor grading by the Watcher on how well you did based on how many of your party members survived.
- Your Size May Vary: The game's most common enemy are t-rexes the size of a tallish human.