The plot resembles some movies and novels of the James Bond series and takes place in the U.S. in an unspecified time period described in game as "199X". During the introduction sequence, the president and his wife are waving at the crowd next to a limousine at the White House in Washington D.C., when terrorists (some flying in using jetpacks) approach the president and his wife armed and dangerous, and, as soon as the screen goes red and gun sounds are heard, they seem to shoot not only the crowd, but also the president and the first lady, who are both presumed dead.

Later, a secret agent working for the American secret service, and known only by the name of Sly, is informed that the terrorists who struck at the presidential ceremony were located, identified, and confirmed to be CWD (Council for World Domination) members. CWD is a secret underground criminal organization with terrorist foundations, involved in drugs and arms dealing and government corruption, and ultimately plotting world conquest. Sly is assigned by the secret service to eliminate the CWD.

Listening to the world's desperate plea for freedom and hoping to protect those he loves most, Sly jumps from a plane towards Washington D.C., and begins his campaign to prevent the terrorists from infiltrating not only the city, but several spots in the U.S., and must also prevent a nuclear missile from launching and striking the Earth.