The game begins with a Furon, Cryptosporidium-136, hovering over a launch site with military personnel testing a rocket. The rocket is launched and destroys the ship carrying Crypto-136, and leaves him fatally wounded. Crypto-136 is later captured by the U.S. Army. Some time later, Cryptosporidium-137 travels to Earth with another Furon, Orthopox-13. Cryptosporidium (nicknamed 'Crypto') comes with the intention of rescuing 136, while Orthopox (nicknamed "Pox") desires to extract human brain stems for study. Crypto arrives at Turnipseed Farm in the Southern United States, where Pox mistakes cows for Earth's dominant life-form. The Majestic agency is alerted to the Furon presence when Crypto decimates an army brigade passing through the area. Pox, communicating with Crypto through a hologram-like device, then reveals to Crypto that the reason he requires human brain stems is because they contain pure Furon D.N.A. handed down to them by Furon scouts eons ago when the Furons stopped on Earth for "shore leave" following a war with Mars, which was rendered uninhabitable by the Furon Empire.