As the Joe and Cobra crafts race to the newly formed channel, two tornadoes travel from the other side of the island and merge into one in front of the channel's entrance. Both sides are caught in the whirlpool.

The Joes parachute into the jungle and catch Major Bludd's forces in what he calls a pincer movement. Lady Jaye suggests to Flint that a small team could get into the temple before Cobra and escape with the weather dominator fragment before Cobra. Flint gives the okay and Lady Jaye, Shipwreck, and Gung Ho, who was ordered to stay at headquarters ("What? And miss a good fight?" he tells Flint) sneak past the SNAKE robots, who are eventually destroyed by the Joes' Pac Rats.

While recovering the component for the weather dominator, Lady Jaye steps on a stone that activates the large stone guardian sitting in the temple.

Cutter radios Torpedo for help out of the whirlpool and tells Cutter that he just got "one mean idea." Piloting the SHARC to the bottom of the ocean Torpedo fires off two torpedoes and shouts, "They don't call me Torpedo for nothing!" The explosion unbalances the whirlpool and both the G.I.Joe Whale and Cobra's craft are freed and land on opposite sides of the partially destroyed reef. Spirit offers to take the WHALE's hydro-sled and try to recover the ion correlator, however, Cutter is leery of the plan, but eventually agrees. Watching Spirit glide across the waters to the island, Torpedo wishes his friend good luck.

Cobra sends into the Palace of Doom a large robot with cobra's head, which has been programmed to retrieve the second component of the weather dominator. Soon the robot and the stone machination are fighting one another.

Spirit lassos the ion correlator and hauls the piece out of the river and onto the shore. Spirit comments to Freedom, his pet eagle, that there is so much anguish over a piece of wreckage. As Storm Shadow attacks Sprit, they fall into the river and over the edge of the waterfall with the fragment from the weather dominator.

Tripwire rushes up to Flint and reports that a large earthquake is approaching their location. As the two monsters continue to fight inside the Palace of Doom, the Joes sneak out. The earthquake reaches the temple and Cobra's forces retreat. Gung Ho and Shipwreck jump across a crack in the earth but by the time Lady Jaye arrives the gap is too large to leap across. Suddenly, the two monsters burst through the temple walls and threaten to crush or push Lady Jaye over the edge. She pulls out a javelin, extends the length and pole vaults across. She doesn't quite reach the other side but Gung Ho catches her and both he and Shipwreck pull her up. "Gung Ho," she tells him, "you're a handy guy to have around." The tremors cause the ion correlator to tip over the edge and is caught by Major Bludd, who is flying a CLAW.

The three Joes find themselves stuck on a column that could collapse at any moment and Lady Jaye calls out for Flint's help. A compressed ladder is launched and the Joes climb across. But the column falls apart and Gung Ho and Shipwreck fall into the depths of the Earth.