The plot revolves around G.I. Joe, America’s daring, highly trained special missions force. The Joes have just perfected a new technology: Mind Interface Remote Control (MIRC), which allows soldiers to flawlessly command vehicles from a safe distance. The title refers to the fact that the two opposing forces, the G.I. Joe Team and Cobra, make use of spies to achieve their objectives. Cobra sends Zartan, to infiltrate G.I. Joe headquarters posing as Shipwreck, and steal the MIRC technology. The Joes send Shipwreck and Snake Eyes to the enemy's camp, after learning about what happened. The Joes then organize an assault on Cobra Mountain and successfully regain the technology, destroying Cobra's base and chopper in the process.
- Although set in its own continuity, Spy Troops: The Movie borrows heavily from themes established in both the comicbook and cartoon versions of A Real American Hero.