Black Major has created a mind controling gas that he wants to sell to Cobra. In order to prove it works he captures Flint and test it on him. But fellow Action Force and G.I. Joe members help rescue Flint after he escapes.
Flint apparently in an extreme panic is hiding behind a tree as several of the Action Force team members hunt for him. He jumps out punches one of the members and runs of into the night thinking, "I know to much, If they catch me I'm a dead man, I know their horrible secrets."
Two days previous on the U.S.S. Flagg: Flint is being bombarded by questions from two "pencil pushers" who are actually executives from the agencies that are a part of Joint Special Missions Force Accords (JSMFA). He goes into a conference room, leaving them in the hallway. Action Force member Natalie Poole, who is assigned to Flint through the JSMFA, tells him that she understands his frustration. GI Joe team member Lifeline, who is also assigned to JSMFA, tells Flint that it is his responsibility to answer those questions, it is part of being the commander. Natalie then invites Flint to join her and Action Force member Dolphin on a kayaking trip. Lifeline agrees that a vacation is needed for Flint to help relive the stress and he needs to accompany him as his doctor.
Two days later in the Black Forest, Germany, Flint, Natalie Poole and Dolphin are loading their kayaks into the river as their German guide makes a suggestion about a nearby former secret World War II base. It peaks the interest of Flint and they decide to follow the guide to the base. As they are walking there the guide falls down a hill and sprains his ankle, Natalie Poole stays behind to help as Flint and Dolphin press on to see the base. As they arrive they see that the site was never cleaned up and that there are some modern fixes mixed in. Out of nowhere 3 Red Shadow Troopers attack Flint and Dolphin. Flint tells Dolphin to run as he fights the three of them. One of the Red Shadow Troopers releases a gas right into Flint's face that immediately knocks him out.
Flint awakens tied to a chair now inside the bunker, where the leader of the now resurrected Red Shadows, introduces himself. Black Major explains to Flint that he uses Lyssazine gas, which is a potent nerve agent that allows years of psychological conditioning and brainwashing to be administered in hours, to control his soldiers. And he plans to use Flint, after he has been completely brainwashed by the gas, as a way of getting Lyssazine gas into the different counter terrorism special forces groups air filters, k-rations, bottled water and medical kits, so they can all be mind controlled by him. It is actually one step in Black Major's plan to control Cobra and the world.
Dolphin comes running back to the river bank where the kayaks are located. Natalie Poole is waiting. Two Red Shadow Troopers are on his trail. Natalie shoots one with her pistol and Dolphin hits one in the head with rock but not before he blows up one of the kayaks with a grenade. The two Red Shadow Troopers recover quickly because they are wearing body armor. But Dolphin has a surprise for them when he pulls out of his kayak a heavy machine gun which kills them.
Back at the bunker, Flint has been going through mind control as Cobra's liaison to Black Major, Interrogator, is watching. Because the Red Shadows can produce the Lyssazine gas in large quantities, Cobra Commander is interested in the results of the tests on Flint. Flint passes out. Interrogator reminds Black Major that his recommendation will be the reason Cobra creates the union between the two organizations. As a Red Shadow Trooper goes to pick him up Flint he attacks successfully, runs out of his room and ducks into a closet where he finds a gun and several grenades, which he gladly grabs.
Later Flint has escaped outside into the forest as Black Major, along with Interrogator chases him in their staff car. As Flint rushes into the dense cover of the forest the Lyssazine gas begins to take effect making everything he sees into a horrific nightmare. Several Red Torches light part of the forest on fire which makes Flint nightmares even worse. Black Major shoots the gun out his hand and Flint just runs in sheer panic.
Dolphin, having heard the fights noise, radios to fellow Action Force member Jammer that Flint is running towards them. Jammer with Action Force member Gaucho arrive in their motorcycle but Flint sees them as scary Red Shadow nightmares and throws his last grenade at them. They jump clear but Flint kicks Gaucho. Lifeline joins the chase, noticing that Flint is having hallucinations.
As everyone is chasing Flint he runs into a mountain cabin. He sits down. Black Major is the first to get to him and he tries to turn Flint to the Red Shadows way, but Flint refuses and fights back. Outside the cabin the Red Shadows are battling the Action Force team. Lifeline gets away from the battle and moves towards Flint. Black Major has been defeated by Flint. But instead of capturing him Lifeline decides to help Flint by sedating him. Black Major sees helicopters filled with Action Force and GI Joe team members arriving and he turns running away. Lifeline just watches him go as Flint sleeps.
Later, Chuckles has arrived along with AF members Blades and Starduster to help clean up. He says to Natalie Poole that they are doing everything they can to keep the lid on this attack since it was the first time that the Red Shadows have officially risen up since they were defeated many years ago.
The next day: Cobra Commander is talking to Black Major by video conference. The Commander tells him that he is disappointed in the outcome of the mission because Flint is no longer any use to them but still very interested in the Lyssazine gas production. So he proposes a financial arrangement be made. Black Major then lets him in on a secret. Which is that he has another undercover agent inside GI Joe that won't be monitored. And it is Natalie Poole. Apparently, the guide who sprained his ankle was actually Interrogator, and along with the Lyssazine he was able to use his skills to turn her into a Red Shadow's agent. Cobra Commander is impressed and decides to make the Black Major and the Red Shadows part of Cobra.
Elsewhere, Natalie Poole is watching Lifeline take care of Flint, when a random doctor walks up to her, he says "I have a tough assignment for you in Fruhlingfeld. Pack for cold weather." Natalie goes blank and walks out of the building.
At a Red Shadows rally, Black Major screams into a microphone that the Red Shadows now have Cobra and tomorrow they will have the world.