A G.I.Joe SHARC lands on a moonlit beach and Polly squawks at Shipwreck and Lady Jaye to move toward cover, but while they crawl in the brush, Shipwreck grabs the parrot and tells him to be quiet since the entire island could be crawling with Cobra agents. Polly agrees to be quiet but bites Shipwreck’s hand and flies away as a man with a machete stumbles toward the Joes. He asks, “G.I.?” Lady Jaye climbs up from the ground and introduces herself and asks if he is Doctor Mullaney, but the man collapses into her arms. She asks Shipwreck if he brought the rations and Shipwreck tells her that he did, but adds that the doctor is going to need more than a candy bar and instant noodle soup.

While sipping on the soup, Dr. Mullaney explains that he was working on a formula that could weaken the bonds between hydrogen and oxygen in water, and, as a result, Cobra could turn a lake, a river or an ocean into a bomb. Lady Jaye and Shipwreck learn that the formula sans one key ingredient is kept at Temple Alpha, Cobra’s central headquarters. Lady Jaye tells the doctor that they are taking him back to the USS Flagg, but before they leave, Mullaney pulls out a neural transceiver and imprints the complete formula into Shipwreck’s brain via electro-chemicals. “You put the formula in there?” ask Lady Jaye, who looks at Shipwreck. “Hey!” shouts Shipwreck. “It ain’t like he flushed it down the sewer.” Dr. Mullaney adds that the formula is in Shipwreck’s subconscious and can be recalled when he is told the password, which he tells Lady Jaye, and Polly listens as well.

Before the Joes and the doctor can leave, a Cobra Firebat fires on them. A missile from the Cobra plane strikes a tree and Dr. Mullaney is trapped underneath. Lady Jaye fires an arrow from her crossbow, hits the plane and destroys the wing with its explosive tip. The Firebat crashes and the Joes remove the tree from Dr. Mullaney’s legs. But as they walk back to the SHARC, another Firebat appears and fires a missile at the group. In the aftermath of the explosion, Shipwreck finds Lady Jaye and Polly, however, Dr. Mullaney is not found.

The Joes make it back to the SHARC and take off moments before a Rattler attacks. Lady Jaye flies between two Firebats and tells her passengers that she believes they are safe. But a Firebat catches up with the Joes and radios Major Bludd, who is flying with a squadron of Rattlers, for assistance in destroying the Joes. But the SHARC finds toward the USS Flagg, which shoots down one of the Firebats. Major Bludd’s group, however, flies in from the opposite side and attacks the SHARC and the USS Flagg. Lady Jaye tells her teammates that they don’t stand a chance so is going to attempt to land. “Don’t attempt - do it!” shouts Shipwreck.

Lady Jaye lands the SHARC near the USS Flagg and Roadblock, who is ordered by Flint, stops shooting at the Cobra Rattlers and throws down a rope ladder to the Joes. But Major Bludd’s attack shots hit the SHARC and the canopy slams down while Shipwreck is still inside. Polly tells Lady Jaye, “Man overboard,” and she orders Torpedo to send a rescue team down to retrieve Shipwreck before the SHARC sinks. However, Skystrikers on the deck of the USS Flagg explode and the Joes scramble for cover from the fire and the Rattler’s attacks, and Shipwreck sinks into the murky depths of the sea.