Set in the fictional cartoon-like city of New Bedford. After Chip Hazard tears off Archer's arm and Archer plugs it back in, the player chooses a campaign. The Commando Elite intend to exterminate every Gorgonite and non-Commando in New Bedford, then destroy Washington D.C. and build a Commando empire. The Gorgonite objective is the opposite: defend all life, preserve freedom, and if victorious, reprogram the Commando Elite with pacifying technology — replacing their chips and uniforms to neutralize them permanently.