Lady Jaye, Clutch and Footloose peel apart from one another and climb into the sky. They regroup and shoot down the Rattlers, however, more Cobra planes appear after the Firebat pilots parachute to safety.

As the Dreadnoks, who consider taking the prisoners to Destro for more money, drive Airtight, Footloose and Flint to Police Chief Zartan's headquarters, they pass by a slave soup line.

And Barbecue, who is in the front seat, slams his foot down on the pedal and forces the car to crash into a ditch while the other Joes punch the Dreadnoks with their hands still cuffed together. The Joes climb out of the car and escape.

Steeler stumbles across a barren land and eventually collapses in a delirious state. Grunt pulls up in an AWE Striker and tries to carry his friend back to the base, but Steeler pushes his friend away and begins to run again. Following him in the AWE Striker, Grunt chases his friend while a Cobra agent flying a CLAW uses a camera to transmit the scene to the Baroness and Layla, who informs the Baroness that Steeler has been bitten by one of Destro's mutated insects which live on the proving grounds and carries the bacteria strain D virus. The Baroness tells Layla that she knows what to do, and Layla curtsies and tells the Baroness, "By your command, Mistress."

Back at police headquarters, Zartan yells at the Dreadnoks for allowing the Joes to escape and the Dreadnoks simply stammer that the Joes didn't have one ounce of respect for the law. Zartan explains that their failure doesn't matter since he will handle the matter personally.

A Cobra Firebat pilot in a Rattler reports the coordinates of the Joes and when Lady Jaye, Footloose and Clutch fly near the Washington Monument, a panel at the pinnacle of the tower folds down, a satellite dish extends out of the tower and three beams are shoot at the Joes. The beams criss-cross and capture the Joes' Sky Hawks inside a net that drains the laser cannons. Destro laughs at the Joes and explains that their power has been drained thanks to his invention, the parasite matrix. The Joes try to eject and blast their way out of the Sky Hawks, but even the power in the guns has been wiped out. Then the net to the parasite matrix begins the constrict and the Joes fall to the ground after Sky Hawks are crushed.

While on the run, Flint discovers that Cobra has turned the Washington mall into a slave labor camp, which prompts Barbecue to reply, "Heckuva way to solve unemployment." The Joes knock out two Cobra troops, steal their weapons and blast the chains between their handcuffs. As they run under the cloak of night, Airtight comments that even if the Dreadnoks are cops, they are still stupid. Zartan appears behind the Joes and fires a flare that signals a FANG to fly behind the Joes. After hearing the pilot demand their surrender, the Flint tells the others, "Know what I say to that? THIS!" Flint fires his gun at the FANG and Airtight shouts: "YO JOE!"

Zartan chases the Joes on a motorcycle, but Flint stops him by shooting a statue of a cavalry soldier that falls down and blocks Zartan's path. However, Zartan is unable to stop so he jumps off the bike before it smashes against the statue and explodes. Barbecue shoots the cannon on a Cobra FANG helicopter and after the pilot jumps out, the helicopter lands on the ground but doesn't crash. Flint pulls the helicopter upright and starts the engine. Blades turn and he pilots the Joes away after Barbecue shoots another cavalry statue, which hooks onto the rails of the pursuing FANG. But the Dreadnoks lift the statue and the FANG continues to follow the Joes.

Inside the White House, a Cobra agent tells his Highness, Cobra Commander, that the prisoners are in the interrogation room and that Destro is unaware that they are missing since he is busy with other business. Cobra Commander hisses an "excccellent" compliment and dismisses the Cobra agent as he enters a control room.

Strapped to a blade on a large fan, Lady Jaye tells Cobra Commander that they are not who he thinks they are, the Joes who have been hiding from him. With a turn of a knob, the fan begins to turn and Cobra Commander threatens them to reveal what they know or his centrifugal persuader will "rattle the answers" from the Joes.

Grunt catches up with Steeler again, but Steeler attacks his friend and the two tumble down a rocky cliff. When they reach the bottom Steeler is somewhat clear-headed and begs Grunt for help, and with Steeler's arm over his shoulder, Grunt helps his friend climb to the top. Steeler stumbles over some bones and Grunt quickly scales the wall, drives the AWE Striker to the edge of the cliff and aims the headlights at the bottom of the ravine. Sliding down to the bottom, Grunt examines the skeletal remains and whispers, "Mother of mercy - they're Joes."

Believing that they were caught in one of Cobra's weapons tests, Grunt bends down and reads the dog tags. The first reads "Steinberg, L." (Clutch) and the next one reads "Graves, Robert W." (Grunt, who knows he is not dead). Steeler picks up the dogtag of the next Joe's dogtag, which states "Pulaski, R. P. O POS 72482011" Believes that he has died, Steeler again runs into the night. He begins to climb up the rocky cliff but stops near the top when he sees a Cobra HISS tank pull up. Layla tells an unbelieving Grunt that they must trust her to take them to the Baroness so that she can help the Grunt.

Meanwhile, Cobra Commander is still not satisfied with the Joes answers, therefore, he releases their bonds while they are still spinning and the Joes fly through a hole in a wall and land against an energy net in another torture chamber. Cobra Commander laughs with glee and tells the Joes that they are about on embark on a great adventure.

Steeler awakens on a couch and Grunt places a cloth on his forehead and tells him to relax and give the medication time to work. Steeler asks if Grunt said something about another world and Grunt confirms the conversation and adds that the Baroness of the parallel world they are in thinks he is the Steeler of her world. But before Grunt can tell him more, Layla enters the room and leads Grunt out so that the Baroness can be with her beloved.

The Baroness sits on the edge of the couch and begins to weep. She kisses Stealer’s hand and a bewildered Steeler asks if she is a Cobra operative. At first, the Baroness is dismayed at the thought, however, she quickly believes that Steeler is suffering from amnesia, one of the side-effects from the bacterial strain. Steeler sits upright and asks for his friend to be brought in since he is quite confused.

Cobra Commander listens to the Joes continue to explain that they are not from his world, and Cobra's leader is so angered by their reply that he chains the Joes up and sends robot boa constrictors to crush them.

Airtight fires a shot at the Cobra FANG and destroys the helicopter, however, the Joes are caught by Destro's parasite matrix. A Cobra agent brings Cobra Commander a message, which states that according to Cobra Commander's spies, Destro has capture more Joes and has attempted to conceal his catch from him. Enraged, he orders the Cobra agent to leave, and as soon as he leaves the room, Footloose, who has been swinging back and forth while Cobra Commander was reading the message, breaks the glass window open and flings the robot snake off of himself and onto Cobra Commander. Screaming in a panicking voice, Cobra Commander crashes against a computer panel behind him and shorts out the snake and knocks himself out as well.

With the rooms power shorted out, the manacles are unlocked and Lady Jaye swings into the control room and kicks Cobra Commander against a wall, knocking him out again. The other Joes swing into the room and all three escape.

The Baroness asks if Grunt and Steeler are lunatics after they have told her their fantastic parallel world tale. But as Steeler places his hands on her shoulder, the Baroness notes that her Steeler had a tattoo on his right arm and not on his left.

And the Baroness covers her face and begins to cry. Grunt tries to offer his condolences and explains that they really are not resistance fighters, merely people who wish to find their friends and then find a way home. The Baroness stands up and tells the Joes that she will help them, however, they must follow her lead.

As Barbecue, Flint and Airtight are delivered to Destro’s lab/throne room, the Baroness enters the room and tells Destro that the Joes have defected to their side. "'Our side' as in Cobra's?" asks Destro. But the Baroness explains that she means their side as one without Cobra Commander. Grunt grabs Destro's arm and begins to explain that Cobra Commander is tired of sharing the throne and is gathering his own army to knock out Destro, who angrily marches out of the room and tells the Baroness to take care of the prisoners. And Grunt gives his teammates a quick thumbs up sign.

The Baroness calls Cobra Commander, who awakens from his stupor, and tells him that Destro is creating an army to unseat him. The Joes and the Baroness catch up with Lady Jaye, Clutch and Footloose, who are retreating from a building under fire, and Flint sees a strange sight. In front of the Cobra Capitol, Cobra Commander and Destro have placed their forces on the opposite sides of the street. Flint asks what is happening and the Baroness replies, "I've just instigated the first Cobra civil war and I don't want a ringside seat for my handiwork."

The Joes travel back to the proving grounds and search for a gateway. Flint finds the portal and Barbecue, Footloose and Airtight jump through the portal, and the Baroness tells Steeler that it appears that she is going to loose him a second time. They slip into one another's arms and Steeler then turns to the dimensional doorway and tells her that no one is really waiting on the other side. Just as Clutch is about to jump into the door, Steeler approaches Flint, Lady Jaye and Clutch and explains that he finally understands that it does matter if G.I.Joe does fight or not. Steeler then adds that he has elected to stay behind. The Baroness walks up to him, grabs his hand and places her head on his shoulder. Grunt walks up to his friend and tells him, "Count me in, too, old buddy."

And before Flint can say a word, Clutch tells Flint that he is staying behind and adds that it will be a challenge to rebuild G.I.Joe. Sighing heavily, Flint tells his solemnly friends, "You know, sometimes you can never go home."

Lady Jaye notices the portal closing closing and pushes Lady Jaye into the doorway and jumps through just before it closes, and the Baroness and three heroes wave good-bye to their friends for the last time.

While Stalker stands near the river, Duke and Doc greet the Joes and help them ashore.

Doc asks about Grunt, Steeler and Clutch and Lady Jaye turns away from Doc and tells him, "They're someplace where brave men are needed. Badly."

Flint walks up to Lady Jaye, places his hand on her shoulder and quietly adds, "Amen to that. Good luck, buddies. You deserve it."