First play the game without using any level passwords to start off at another point in the game other than the the first level. Don't lose anyone for the entire game. At the asteriod levels, beat each characters' levels so that they all have a chance to fight Magneto. Then chose anyone to beat him. After that there'll be a ending better than the regular one (where the plane flies up to the asteriod and Capcom thanks you for playing).The better ending is slide show sequence where the plane flies up,next you see the hatch open and the non playable X-men characters will appear.Thne they'll be illustrated shots of the playable and non-playable X-men in pairs(Rogue & Gambit is one) except for Wolverine.
Defeat Juggernaut
When your at the Juggernaut, choose Wolverine as your character. Jump on the platform and wait for Juggernaut to run buy. Run behind him and hit him 4-5 times, then run to the opposite platform. Keep doing this until he dies.
Defeat Magneto
To easily defeat Magneto, use Wolverine. Stand in the corner until Magneto starts to bring up the debris. Walk over to him and use the jumping upper-cut move. This will knock off the debris and hit Magneto. Repeat this until he's defeated.
Defeat Omega Red
When choosing an X-men to fight Omega Red choose Beast. When the level starts position your character under the first platform. When Omega Red lands near you press up punch or over over punch, this will knock Omega Red down. Jump on top of the platform until he goes back up then repeat the process.
Extra Life With Psylocke on First Level
When the first door opens and a guy comes quickly press Forward, Forward, Y. Then when he gets up make sure he does NOT move from that spot! While he is still in the spot hold down and then Jump and press the Y button{while still holding down (If you did it right you will get a plate that has a X on it.) You will have to get three of these to get a extra life}To get the second one walk towards the little cliff just before the second door. When you get to the cliff just before you walk off jump then press the Y button. To get the last one you will have to beat the robot boss and when the ground shakes and falls there will be these things you'll have to jump over on the last one the X-plate will be right by it.When you get these all you'll hear a funky sound.