Real American Hero, Snake Eyes and Scarlett would be reunited upon G.I. Joe's reinstatement, and the two again became engaged. Snake Eyes is involved in many skirmishes with Cobra, including altercations with Storm Shadow, the return of Serpentor (in which Snake Eyes was injured by a grenade blast but quickly recovered), Snake Eyes' triumph over the Red Ninja leader Sei Tin (which gave Snake Eyes control of the Red Ninja clan), and a close-call defeat at the hands of the heavily armored Wraith. The team is then reduced to a smaller unit, and when Snake Eyes, Scarlett, and Duke get into trouble, a shadowy cabal of generals known as "The Jugglers" has Snake Eyes and Duke arrested. However, Scarlett meets with Storm Shadow (who had broken free of his mind control), and they rescue Snake Eyes and Duke from a convoy. They escape to Iceland and hide out with Scanner, however they are tailed by former Coil agent Overlord, who fatally injures Scanner and locks the Joes in a bomb shelter. In his last moments, Scanner activates the Icelandic station's self-destruct mechanism, killing Overlord in the blast and saving the Joes. The team then assists Flint, Lady Jaye, and General Philip Rey in dealing with a new menace, the Red Shadows. When the Red Shadows attempted to assassinate Hawk at a mountain camp, Snake Eyes sends his apprentice Kamakura to get Hawk to safety. Snake Eyes would later help in defeating the Shadows before their plot could be set into motion, even fighting leader Wilder Vaughn, who escapes. Snake Eyes and Kamakura also travel to Asia, to assist Storm Shadow in finding his apprentice, who had been kidnapped by the Red Ninjas. Snake Eyes helps Storm Shadow defeat Red Ninja leader Sei Tin, but the mission is a failure. Snake Eyes relinquishes control of the Red Ninjas to Storm Shadow, who in turn leaves his clan in T'Jbang's care. America's Elite Snake Eyes is reactivated as a member of the team in G.I. Joe: America's Elite, along with Stalker, Scarlett, Flint, Duke, Shipwreck, Roadblock, and Storm Shadow. With their new covert status and reduced roster, they continued to track down Cobra cells and eliminate them, from their new headquarters in Yellowstone National Park code named "The Rock". When Vance Wingfield seemingly returns from the grave, and drops deadly satellites onto major metropolitan areas using equipment supplied by Destro, Duke, Scarlett