Pilot Episode
The Jo's storm COBRA Castle! Cobra hits the GIJoe team on two fronts—at the North Pole and in the Amazon! The Joes fight off hordes of new-style BATs and deploy some new hardware of their own. The Amazon supply depot is destroyed and Duke is nearly killed by Destro’s arctic trap! Duke decides that it’s time for a change in tactics. If COBRA is to be defeated, the team has to go “off the gridâ€.
After hacking into the Sigma 6 computer and infecting it with a virus, COBRA sends the Dreadnocks on a rescue mission to free their leader, Cobra Commander. Meanwhile, Duke visits General Hawk in the hospital, and Hawk's son, Scott Abernathy, draws some unwanted attention after hacking into COBRA's computer in an attempt to perfect an A.I. system he's been working on.
The Power Stones are revealed! It seems that there are mysterious natural stones that have amazing technological powers that both Cobra and GI Joe are on the hunt for. In this episode, Zartan finds a Power Stone in the deep jungle and it's up to Spirit and Snake Eyes to team up to stop the evil master of disguise!
The vacation episode! The Sigma team decides it's time for some R&R and they got to Las Vegas for some time off. As soon as they get there, though, they see that Destro is using his casino as a front for developing a super laser. Scarlett and Tunnel Rat must infiltrate the casino and stop Destro before he can finish his master plan!
It's Ninja versus Ninja in this episode. A Power Stone is discovered in a temple on Mount Arashikage and Storm Shadow goes to collect. A massive battle ensues as Snake Eyes takes on his sworn enemy and blood brother Storm Shadow for possession of the Stone. Meanwhile, Jinx and Kamakura show the Dreadnaughts that it's not good to tangle with a deadly dup of Ninjas!
Following the attack on the Sea Titan, Sigma 6 plans to sneak into a Cobra base in order to find out what they are up to and to find the Dragonhawk. When Lt. Stone's position is compromised and Sigma 6's position is betrayed, a risky choice is made that involves launching a missile at the Cobra base even if it destroys everyone and everything in it.
Cobra Command plans a heist to steal a nanotechnology sample from the Central Museum and Sigma 6 moves in to stop it...but waiting for them is Destro, who uses this opportunity as a chance to test his new "Brain Ripper" mind control device! Hi-Tech is the only member of Sigma 6 left standing...can he and his latest gadgets stop Destro and his insidious Mantis Mech all on his own?
When Overkill gets hold of a top-secret biochip, he's able to integrate his synthetic biology with the power of the machine and build a powerful body to battle Sigma Six. Then he tries to steal the remaining chips and turn the world into an electronic extension of himself, and the unlikely pair of Hi-Tech and Spirit is sent to stop him.
With the construction of two Terrordromes at the North Pole and the South Pole, Cobra Commander uses a weather-controlling machine in order to hold the world for ransom after Baroness and Storm Shadow freeze the world leaders. When it comes to the Terrordrome at the South Pole, Snake Eyes fights Firefly while Jinx, Kamakura, and Tunnel Rat destroy the weather-controlling machine there.
This feature film takes the first five episodes of the series and completely revamps the storyline. Team leader Duke is now a fresh recruit who must assemble a Joe team (who sport Sigma suits, the latest in body armor) and battle the forces of Cobra. "First Strike" also posits the curious idea that the two previous direct-to-DVD Joe releases (2003's "Spy Troops: The Movie" and 2004's "Valor vs. Venom") happened some 20 years before the events that take place in this movie.