X-Men 2: Clone Wars/Avalon

Avalon (also known as Astroid M) is Magneto's floating fortress. The first stage is the Asteroid Surface, the second is inside the actual Avalon, the third is an elevator shaft, the fourth is a showdown with Exodus, and the fifth is Magneto's quarters, where you face him as a boss.

Fabian Cortez
After he breaks in from the background, he remains on the far right side of the screen the entire time. Using his jetpack he moves up and down shooting his gun in fixed intervals. Cyclops or Wolverine are good choices for this boss.

Exodus
Exodus spends most of his time floating in the center of the screen. He shoots out energy beams using his hands which can go directly down or diagonally either side. He also occasionally shoots beams at the walls which shake the whole room and will injure the player unless the jump from the floor before the beams hit the walls. As he is progressively defeated he will move to one of the walls either to the left or right and destroy the floor beneath him, creating an damaging obstacle that characters like Beast, Wolverine and Psylocke can easily fall into given they need to jump at Exodus to attack him. Best strategy is to have Nightcrawler stand directly under Exodus and simply teleport up (roughly half-charge) to attack - he will teleport through any directly down attack Exodus may make and all other attacks miss him.

Magneto
There are two parts to this boss fight. Magneto will always float at the top of the screen. The first part is running away from him, where you must break through certain walls as you run to the right. As you run, he shoots beams of energy in fixed intervals. Eventually you come to a wall that you cannot break. You must distract him so he shoots beams at you but misses so he hits the wall. After the wall is hit numerous times, you move on to the second part of the fight. The second part of the fight requires you to knock Magneto onto a platform. All you must do is hit him to the right, and he will slowly decend onto the platform. His only attacks are single energy beams. Wolverine is recommended.