In the movie, Cobra Commander has been transferred from the FLAGG to another high-security prison in Germany alongside Destro, where he is being force-fed a paralyzing drug whilst floating in a water chamber. He is soon broken out by Storm Shadow and Firefly, but Destro is left behind and Storm Shadow is injured as the base is destroyed. After sending Storm Shadow off to the Himalayas to heal, Cobra Commander retreats to his own base of operations, where he meets with Zartan (still disguised as the President). They develop Project Zeus, a super weapon, which uses kinetic bombardment and targets several prominent cities. Cobra Commander demonstrates the magnitude of the weapon's power in front of the world's leaders by demolishing London. The Joes are able to stop Cobra Commander before he unleashes the full power of Zeus, but the terrorist leader escapes after the deaths of Zartan and Firefly as well as the betrayal of Storm Shadow.