The reset button at the end of Mojo's Crunch
Mojo dies, the screen doesn't end, and the player wanders right looking for a door that isn't there. This is the part of the game that ate people's afternoons in 1993. Professor X tries to warn you back in the Danger Room ("reset the computer"), but most players took that as flavor text.
Attack the big monitor at the right end of the stage, smash it, wait a beat, then tap the physical Reset button on the console. A quick tap. Hold it and the game does what Reset buttons do, booting back to the title screen and erasing the run. After the soft reset the screen turns black, fills with binary, and lands on "VIRUS PROGRAM SUSPENDED". A cutscene with Psylocke and Beast plays, all four X-Men come back at full health, and the Blackbird shows up in the Danger Room ready for Asteroid M.
Right here on SEGA Play, the emulator has a Reset button in its control bar, and that's the one you tap after smashing the monitor. On a SEGA Nomad the reset wasn't wired in at all, which is how this became the rare game you can't finish on certain hardware.
Boss strategies that hold up
Juggernaut
He's only hittable on the head, and only while he's standing still. Everything else bounces off helmet metal. The loop: wait, jump over him, clip his head on the arc up, land, repeat. A savage warrior jumps in from the right occasionally; while one is on screen, Juggernaut won't charge, so the room is briefly safe. If you dodge his charge twenty times without taking a hit, he actually runs off the platform edge and auto-defeats. That's the patient-player ending and it works. The Lighthouse rematch is the same idea, just faster, and now he punches.
Apocalypse
Three things he does: absorbs energy (untouchable, the column hurts you), punches (shrinks afterward, vulnerable for a beat), releases an energy burst (shrinks, vulnerable). The trick is in the geometry. Jump toward him, then veer away once you clear his shoulder. He'll release the burst, you'll land clear, you hit him as he shrinks. When you cross his sprite, walk through him. Don't jump, because the absorb column kills jump arcs.
Nightcrawler skips all of this. Wait for the punch wind-up, Bamf out, Bamf back onto him. The cloud sits on him and grinds him down passively.
Magneto
The whole fight is built around one window. Magneto alternates a two-handed beam (shield up, you can't touch him) with a one-handed beam (shield drops, he plants, you have three to five seconds). That second one is the only time he takes damage. Five mutant power hits end the fight, or fifteen-ish regular ones if your energy bar is dead.
The opening salvo is five magnetic orbs that float for four seconds, then home in straight to wherever you're standing the moment the float ends. Most of your roster reads positions and prays. Don't bother with assists either; they bounce off him. If he hits you three times in a row, swap to another X-Man on the same life, because at that point you've already lost the read.
Picking a character and when to swap
You pick a starter on the difficulty screen, but the run depends on who you're holding in reserve. Substitutions are limited per zone: three in Savage Land, Shi'ar, and Asteroid M; two in Lighthouse and Ahab; one in Mojo's Crunch. Walk into Mojo with the wrong four and you can't swap your way out.
Wolverine's healing is the only way to mend health mid-zone without an item pickup. Watch the Berserker Rage threshold though: if his energy bar hits zero while the claws are out, he flails uncontrollably for three to five seconds, hurting himself and sometimes walking off a ledge. Sheath the claws at one-fifth bar and you'll never trigger it.
Cyclops barely spends energy. He fires more mutant power shots per zone than anyone else, his optic blast rebounds off flat surfaces for free, and his jump is the tallest in the game. That last bit pays off on the Lighthouse climb and the Magneto platforms. Don't take him into Mojo though; hand-to-hand he's nothing.
Gambit's job is range, but his crouching pose in the Shi'ar level is taller than everyone else's, and trooper blasts that sail over Wolverine clip him in the forehead. Use his crouching attack animation, which drops his head, instead of a plain crouch.
Nightcrawler is who you save for impossible windows. Bamf is the only sure dodge for Magneto's opening five magnetic orbs, and a clean way out of Juggernaut's charge if you don't want to time the jump. He also teleports through walls in the Lighthouse to skip the Juggernaut rematch entirely. Standing attacks are weak, so don't grind regular fights with him.
Stage skips that work
X-Men ships with a stage select and hides an undocumented stage-skip glitch on the first three zones. Playing it online covers both cleanly.
Level select
The official stage skip, put in by the developers. Reliable on any setup with one footnote: a second controller in port two breaks it.
When "Press Start" shows on the title screen, hold +L+Space+Enter. Keep holding until the difficulty screen appears.
Pick your difficulty and character, then walk right. Eight panels line the back wall, one per stage. Crouch in front of one and press Space to drop into that stage.
Gambit glitch
Pick Gambit, walk into a zone, and as the screen darkens at the entry, hold L. Instead of starting the level, Gambit goes into his charging pose; release and you're back in the Danger Room, the stage marked complete. Works on the first three zones only. Savage Land takes two skips (the main area and the boss section count separately), Shi'ar goes in one, and the Lighthouse skip triggers at the door. From Ahab's Future World onward the glitch is gone.
Don't lose the glasses in Excalibur Lighthouse
The mirages on this stage are clones of you. Wolverine throws his own punch, Gambit swings the same staff, Nightcrawler kicks from a crouch, and Cyclops fires his optic blast. They float for a second before materializing, and nothing you hit them with does damage until you pick up the glasses tucked inside the lighthouse itself.
Get hit too many times and the glasses fly off. From that point you can't kill mirages and you can't progress, which means walking back through the mirage corridor empty-handed for a second pair. The safer play is bringing Nightcrawler into this zone. Bamf dodges the clone attacks entirely instead of trading hits, and every contact is a chance for the glasses to come loose.