In order to fight Bahamut Overdrive, the player must choose the following options:
- "Rescue the research center"
- "Surrender and fight later"
In the last stage, Big Battle, the leader of the rebellion, Colonel Bahamut, succeeds in merging his spirit with the corporeal qualities of the alien, which results in him transforming into an all-powerful symbiotic being.
The creature first manifests as a muscular human/alien hybrid radiating with energy. The beast has superhuman speed and agility, being also able to project blasts of its own energy in order to attack from a distance. However, the entity results to be very unstable and unable to contain its own power, ending up losing control and ultimately transforming into an amorphous, two-headed, giant monstrosity. As it grows more unstable, it mutates once again into a beating heart surrounded by tormented faces that pulsate outward when the heart is hit.
- This boss also appears in the Game Boy Advance game Contra Advance: The Alien Wars EX, a handheld port of Contra III: The Alien Wars; however, this is not a canonical appearance and has nothing to do with the plot. Likewise, Colonel Bahamut does not appear in this version, only the already transformed boss. The inclusion of the Big Battle stage was only to replace the overhead-view Sheer Cliff stage from the original game.