Framed for crimes against the country, the G.I. Joe team is terminated by Presidential order. This forces the G.I. Joes into not only fighting their mortal enemy Cobra; they are forced to contend with threats from within the government that jeopardize their very existence.

From the Egyptian desert to deep below the polar ice caps, the elite G.I. JOE team uses the latest in next-generation spy and military equipment to fight the corrupt arms dealer Destro and the growing threat of the mysterious Cobra organization to prevent them from plunging the world into chaos.

Russian and British submarines with nuclear missiles on board both vanish from sight without a trace. England and Russia both blame each other as James Bond tries to solve the riddle of the disappearing ships. But the KGB also has an agent on the case.

The Cold War has just heated up! CIA Agent Bob Taylor (Charles Napier) arrives in Moscow with his new wife Susan (Kimberley Kates) with a highly secret video tape of Russian missiles leaving an unknown base near Moscow under the cover of darkness. Are these missiles destined to be aimed at the US or are they being smuggled to a terrorist organisation. The Americans need to know where these missiles are going, the only person who can help them discover their destination is Armstrong (Frank Zagarino) an ex buddy of Bob who now trains an elite Russian anti-terrorist squad under the command of Colonel Zukov (Richard Lynch). Zukov is from the old guard, corrupt, ruthless, and will stop at nothing to gain control.