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Bonus characters and costumes:
Beat arcade mode using the following characters to unlock bonus characters and costumes:

Use - Unlock:
Gambit - Bishop
Bishop - Blob
Phoenix - Dark Phoenix
Betsy - Psylocke
Any Mutant - Third Costumes

Unlock everything:
At the main menu, hold L1 then press Right, Right, Left, Left, Down, Up, Circle.

Fight as Bastion:
Successfully complete the game story mode as Magneto without losing any matches to face Bastion. Defeat Bastion to unlock him as a selectable character.

Fight as Bishop:
Successfully complete the game in arcade mode as Gambit to unlock Bishop as a selectable character.

Fight as Blob:
Successfully complete the game in arcade mode as Bishop to unlock Blob as a selectable character.
Information in this section was contributed by The Guardian.

Fight as Psylocke:
Successfully complete the game in arcade mode as Betsy to unlock Psylocke as a selectable character.

Fight as Dark Phoenix:
Successfully complete the game in arcade mode as Phoenix to unlock Dark Phoenix as a selectable character. Alternately, successfully complete the game in story mode as Magneto.

Fight as Sentinel A:
Successfully complete the game in arcade mode as Cyclops.

Third costume:
Successfully complete the game in story mode to unlock that character's third costume.

Sixth costume:
Defeat all ten fighters in time attack mode in under fifteen minutes to unlock the sixth costume for the fighter you selected.

Nightcrawler: Play in the Dimensional Rage
When in training mode as Nightcrawler, turn on "Infinite Specials" then perform the Dimensional Rage technique. You will be in the Dimension for the technique. Perform a different special other than Dimensional Rage and make it contact. This will cancel Dimensional Rage and leave you in the darkness. To exit, perform the Dimensional Rage again and let it finish properly.

Apocalypse appearance
In the Crypt level, fight in the lowest area for a chance to see Apocalypse. His sarcophagus rises out of his tomb and separates, leaving him floating in the air. He laughs, then goes back inside. This is sometimes triggered by good fighting.

Save special move
When you are fighting against Bastion, Sentinel A, or Sentinel B, and they do a move to put your special on hold, pause game play until the move against you wears off. You will be able to use your special without wasting time.

Seventh costume
Select team mode and choose to fight with eight characters. Defeat all of the your opponent's team by using two or less of your own fighters to unlock the seventh costume for the character(s) you used.
Wolverine gets his original yellow/blue/black costume.
Phoenix gets a red/gold costume similar to Dark Phoenix.
Juggernaut, Gambit, and Psylocke get a costume similar to their comic book original.
Beast gets a blue costume with a yellow X on his chest, and he also has a helmet.
When you chose the seventh costume for Cyclops, Wolverine, Betsy, Juggernaut, Sentinel A (Sentinel), Gambit, Storm, Sabretooth, Rogue and Magneto, they will most commonly appear in their costumes if they were in a "Vs." series game (Marvel vs. Capcom: Clash Of The Superheroes, X-Men vs. Street Fighter, X-Men Children Of The Atom, Marvel Super Heroes vs. Street Fighter).

Eighth costume
Win forty matches in survival mode as any character.

Classic costumes
Some characters have classic outfits that resemble the classic X-Men characters:
Wolverine: Costume VII
Betsy: Costume VII
Forge: Costume VI
Gambit: Costume V
Juggernaut: Costume VII
Magneto: Costume VII
Nightcrawler: Costume VII
Sabretooth: Costume III
Rogue: Costume VI

Ending sequences
There are three possible endings in the game in story mode.

Regular ending (Magneto's Victory): Defeat Bastion as Magneto.
Alternate ending (Phoenix's Victory): Lose the Magneto vs. Bastion fight and you will go to the Phoenix vs. Bastion fight. Defeat Bastion as Phoenix.
Secret Ending (Fury of Dark Phoenix): Get a "Perfect" victory in the Phoenix vs. Bastion fight. This will also, unlock Dark Phoenix as a playable character.