X-Men 2: Clone Wars/Phalanx Flagship

The final level in the game is the infiltration of the Phalanx Flagship. The first part of the stage is ascending the trap filled ship with a Phalanx General as the boss. The second part of the stage is an elevator fight. While standing on a platform, you are attacked by various robots and then you fight Deathbird as a boss. The third part of the stage is the clone factory itself. The final segment of the stage is the fight against the Brood Queen.

Phalanx General
At first glance this boss is nothing more than a bigger normal enemy you faced before reaching him. The General has beams that he can shoot across and diagonally, but this time he can turn into a circle of balls and teleoprt across the room. He has transformations similar to Brainchild's, and isn't too hard either.

Deathbird
This boss's only attack is a cloud of needles she throws. She occasionally swoops in, and when she does you must hit her before the leaves the screen again. When she throws the needles it's easy to dodge. Sometimes when she appears she doesn't even attack. Pretty much every character except Magneto would be useful here.

Brood Queen
This is a very intense boss fight that requires quick reflexes and thinking. She emerges from the right in an explosive entrance, and you must always remain mobile unless she stops. It's important to dodge her potent beams. When you defeat her, remain aware, because you will be chased by her claws when she's dead.

Clone Wars
The final fights of the game are against clones of your playable characters. They contain all the powers you have become familiar with over the course of the game. Use strategy and remember the strengths and weaknesses of each (see Characters) and you should win and beat the game!

Magneto Clone
There is a secret extra boss — a clone of Magneto — that is not normally accessible.

Steps to unlock:
 * 1) Defeat 5 clones of other X-Men, starting with the one that's copied you. This does not work every time — testing results are inconsistent, suggesting either a randomness element or some unknown condition that sometimes gets fulfilled by accident. But known successes have reported defeating 5 clones and/or your clone (first or otherwise), so the best bet is to cover all the bases.
 * 2) Go down to the bottom of the area (where the Brood Queen's claws disintegrated after chasing you) and attack the wall on the left. It will explode in a smiley face / helmet pattern.
 * 3) Go up the right-hand shaft and into the second corridor (the one with a narrow dead end) and attack the wall at the end. The wall will shatter and you will be able to reach Magneto Clone in the next room.