Recondo hears the whining of the hyenas and tells Rock 'n' Roll, who is ready to fight them, that if he takes one down, three more will tear him apart. Therefore, the Joes conclude, it's best if they retreat. Duke tells the Joes that he will take the rear position and the Joes run onward. As the hyenas come closer, all of the Joes swing across a river, but Duke remains behind to fire a few shots to scare the creatures. As Duke runs toward the river, he is caught in a trap when a rope that loops around his ankle and pulls him up into the air. The hyenas jump up at Duke and try to bite him.

Seeing his friend in trouble, Snake Eyes swings back over the river and is ordered by Duke to go back, however, Snake Eyes attacks the pack of hyenas and hands Duke a knife so that he can cut the rope around his ankle. Extremely angry about Snake Eyes disobeying his orders, Duke yells at Snake Eyes, however, Duke's anger melts and tells his teammate that if Snake Eyes doesn't say anything about it, then neither will he. Snake Eyes gives Duke a thumbs up, signaling his approval of the deal.

As the two Joes head toward the river, Copperhead and several Cobra agents drive by and just as they are about to use the Joes as target practice, Recondo, Snake Eyes and Rock 'n' Roll swing over the river and knock the Cobra agents into the river. Snake Eyes and Duke join the fight and the Joes defeat the Cobras.

Stealing the Cobra agents' uniforms, the Joes pretend that they are the enemy with Snake Eyes as their prisoner. When they arrive at the base Recondo knocks Copperhead out, guides the Water Moccasin into a port and explains to the guard that Copperhead caught a contagious strain of the sleeping sickness in the jungle. The guard retreats after telling the Joes to take Copperhead to the infirmary before the whole base is contaminated.

Duke leads the Joes into the Vulcan Machine's control room and they overhear Cobra Commander listing the cities that could be used as the test target. However, when Rock 'n' Roll hears Cobra Commander mention Los Angeles, he tells Duke, "No way is he going to ace my hometown." Duke agrees and leads the Joes in the attack on the Vulcan machine.

Before Zartan could use Dr. Shakoor as a shield, Scarlett sends another flaming arrow at the roof and the sunlight causes Zartan to change to a painful shade of blue and he retreats. Rock 'n' Roll removes the headband from Shakoor and leads the doctor to safety. As Duke and the other Joes stand before Cobra Commander, Cobra's leader threatens to cease their attack or the entire United States will be turned to ashes. "Surrender, my Grandmother!" replies Duke before he and the other Joes begin shooting at the cannon. Scarlett destroys the control panel with a shot from her crossbow and Cobra Commander retreats.

However, the remaining energy in the cannon fires at the Earth’s' core and lava begins to spew from the Earth and flood the temple. The Joes run back to the Water Moccasin used to enter the base and as Copperhead awakens, Duke tosses Copperhead into the water after explaining that all the dead weight needs to be thrown off. Meanwhile, Cobra Commander is carried away on a Water Moccasin and swears that he will have his revenge on G.I.Joe.

As the Joes drive away, they are stopped by Ripcord, Cutter and Wild Bill who are in a WHALE. Duke tells the Joes on the WHALE to hold their fire when Duke and the others are mistaken as Cobras from a distance. After Ripcord asks what happened, Rock 'n' Roll begins to explain: "Well, first, we ditched the rhino that was chasing us, then Snake Eyes trashed a pack of hyenas and then after that - "
"Huh?" ask Ripcord and Wild Bill.
"I got the feeling this is goin' to be one whopper of a story," states Wild Bill.
"Wild Bill," Duke replies, "you don't know the half of it."