The game takes place during December 2634 A.D. A disturbing distress signal from General Hal is received, who was on his way to South America in preparation for the GX Army's 7th military maneuvers, reporting that the GX Army has suddenly revolted. The top branch of the federation forces calls forth Bill and Lance to investigate the situation. They arrive at the base ruins, only to find out that the GX Army's troops were being possessed by the same kind of mutated creatures they fought at Galuga (in the original Contra). Thus, the situation becomes grimmer taking into account the fact that Bill and Lance are killing their former comrades-in-arms. After a fierce battle, ultimately leading up to the alien nest, the alien invasion was once again thwarted. Naval records concealed the events of the mission, with a cover story being told to the public that the GX Army's destruction was the result of an accident caused by a discharged weapon.
