There are three possible endings in the game in story mode:
Regular ending (Magneto's Victory): Defeat Bastion with Magneto.
Alternate ending (Phoenix's Victory): Lose the Magneto vs. Bastion fight and you will go to the Phoenix vs. Bastion fight. Defeat Bastion with 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.