While on an island, Lady Jaye and Shipwreck are on a rescue mission to save Professor Mulaney, a scientist who claims of developing a new weapon to turn water into a bomb. When they find him, he implants the secret formula into Shipwreck's brain, which can only be released by a secret code word he gives to Lady Jay. Shipwreck passes out trying to escape after a Cobra assault and wakes up six years later in a place called Springfield, with Mara as his wife and a daughter named Alfea. G.I. Joe has won the war against Cobra, but he tries to find out how in the years he's missed.