Two years after the Alien Wars, Earth is at peace again. However, the Black Viper returns after being defeated previously. She caused mass destruction over the planet. Strange readings are detected in the Galuga Archipelago. The Contra Force sends Bill Rizer, Lance Bean, Mad Dog, and Scorpion to investigate the readings. They found the readings that came from the Black Viper's main base. The 4 Contras battle the Black Viper's army, which consists of aliens, robots, and mutants. Later they find out that the Black Viper's host was none other than Jagger Froid inside her body. But, however the Contras managed to destroy the brain of Jagger Froid inside Black Viper and save humanity once again.