Half-dressed as a security guard, Zartan joins the Dreadnoks as they toss papers aside while looking for the blueprints of the matter transmutor.

After Ripper finds “the bloody blueprints” and Buzzer grabs the device, Zartan and his crew cruise under a bridge aboard a Cobra Water Moccassin driven by Copperhead.

Dissatisfied with the speed of Copperhead’s Water Moccassin, Zartan decides to split up with the Dreadnoks and agrees to meet them at the Redwood base. Inside a tree, Destro shows Cobra Commander a video that demonstrates the power of the matter transmutor. The rays from the transmutor turn a rock into an apple and transforms an iron safe into a fragile box made of tissue paper.

Cobra Commander tells Destro that he’s has the idea, however, what he doesn’t have, he tells Destro in an annoying tone to the arms dealer, is the matter transmutor device.

As Destro subtly insults Cobra Commander’s decision to hire Zartan to steal the device, Cobra Commander walks out of the room with the Baroness and tells Destro that he had better watch his attitude, and Destro crushes a metal remote control in his hand.

Sitting inside a Mauler tank, Steeler complains to Lady Jaye, Clutch and Grunt about the being on the Joe team and its toll on his personal life. However, they tell him to stop complaining since they have all made sacrifices. Steeler relents and still presses the matter of their mission, which feels like a wild goose chase. However, Steeler picks up a boogey on his radar.

Flying above a forest’s treetops in a Cobra Viper hang glider, Zartan shoots at Flint, who pursues the mercenary in a Falcon glider. After each opponent exchanges shots and insults, Flint flies into a tree and Zartan calls out to Flint, “What’s a matter old boy? Up a tree, are you?” Raising his rifle, Flint yells back, “Laugh this off, laughing boy!” Flint hits Zartan’s hang glider and the Viper glider falls toward the ground.

Ripper catches sight of Zartan so he hops in a Cobra Stinger and drives across a shallow stream to catch up with his boss with Buzzer and Torch in tow. Upon a hill, Lady Jaye watches the Stinger drive by, radios Steeler to “swing into plan A,” and zooms forward in an Armadillo while telling Grunt and Clutch to hang on to their teeth.

As Lady Jaye pursues the Dreadnoks, a tree suddenly collapses and blocks the Dreadnoks path, and while Zartan flips out of control in the air, they abandon the Stinger and Steeler drives a Mauler over the tree and crushes their vehicle. Debris from the Stinger flies upward and puches through the wings of Zartan’s Viper glider, causing him to fall to the earth and lose the plans. The blueprints fall to the ground and just as Grunt misses catching them, Clutch snags the plans and falls into the river.

Steeler points his Mauler’s cannon at Zartan and tells him that since the Cobra agent is outgunned, he might as well surrender. However, Zartan tells Steeler that he will never surrender, grabs the Stinger’s missile rack and fires all of the missiles. They strike the Mauler, but Steeler jumps clear. Barely. Turning to the fiery remains of his tank, Steeler tells himself in a half-haunted voice that if he was half a second slower he would be “vapors.”

“Noooooooo!” screams Cobra Commander.
“Yes!!!” yells Destro.

They watch Zartan and the Dreadnoks enter the Redwood base and Destro tells Cobra Commander that retreat is their only option. The sides of the tree that served as Cobra’s base split to reveal a rocket, and the Cobra elite blast off and escape from the Joes. As Flint stands dumbfounded, Steeler tells Flint, “We can tell our grandkids about that, Flint, if we live to have any.”

Inside a G.I.Joe WHALE, Footloose, who is sitting at a table with Barbecue, Grunt, Clutch and Steeler, ask Airtight why the brass at headquarters expects that Cobra will try to steal the blueprints again, but Steeler throws down his playing cards and asks in a depressed voice, “Who cares?”

Seeing the battle with Cobra as one endless battle after another, Steeler tells the others that he is quitting the team. Clutch tries to tell him that he is simply spooked. Barbecue sympathizes with Steeler explaining that sometimes “there’s ne’er an end in sight.” But as soon as Steeler asks why the Joes bother to fight if no one is going to win, they quickly begin to argue with Steeler, but Cutter cuts the debate short as he announces that they have reached the reandevouz point.

A train flies across iron rails and inside one of the cars Lady Jaye and Flint compliment Dr. Renault’s idea of disguising her transmuter research team inside ordinary grain cars. General Wagstaff, Dr. Renault’s military liason, meets the saluting Joes and Dr. Renault then asks for the plans. Flint immediately tells her that they don’t have the plans and that she is supposed to know this piece of information.

General Wagstaff pulls out a gun and removes his mask to reveal himself as Zartan and the Joes watch Dr. Renault rip away her disguise, and the Baroness, pulls off an earring and tosses it to the ground in order to create a smoke cloud. The Baroness tosses Lady Jaye out the door and as Flint stumbles forward to find her, he is pushed from behind by Zartan. The Joes catch beams that part of a wooden bridge and as several Joes climb out a WHALE to help thier friends, Cutter is ordered by Flint to tell the other Joes that they need to rescue the kidnapped Dr. Renault and General Wagstaff.

Copperhead arrives at the bridge and sees that Steeler is carrying the plans so he climbs out of his Water Moccassin and begins to climb the bridge. He grabs Steeler’s leg, but Steeler kicks Copperhead’s hand and causes the matter transmutor to be fired in a widespread range. The bridge turns to glass and collapses into a river, but a dust cloud swirls over the Joes heads and they remain unconscious on the ground.

The Joes climb out of their black outs and begin to explore thier surroundings, which have radically changed. There is no longer a forest or a river, however, the area is still the same, Flint points out while showing the Joes a chasm that contained the river. Grunt, Footloose, Flint, Lady Jaye, Airtight, Steeler, and Clutch then begin their long march back to headquarters.

Steeler is bitten by a large pink and black bug that flies onto his neck and as he slaps his neck and kills the bug, he examines it and tells the Joes that he’s never seen anything like it.

Flint looks up into the sky and sees that the buzzards have company - Cobra CLAWs. The Joes run across the barren land and Clutch tries to call Joe headquarters, but all he hears is static on his headset. Barbecue helps carry Steeler into a cave and the CLAWs fly away.

Footloose examines the cave and finds an AWE Striker and also finds the keys. Lady Jaye asks Flint what is going on and Flint tells her that he doesn’t know, but all he cares about is the condition of the AWE Striker. Pumping the pedal, Footloose finally makes the engine roar and after zooming around the cave and screaching to a halt in front of the Joes, they all shout, “YO JOE!”

However, the Joes’ luck begins to turn sour as the AWE Striker’s engine dies just as it reaches the top of a hill. Fortunately, a general store is at the bottom of the hill. The Joes walk inside and buy eight motorcycles. As Flint pays for the bikes with cash, Barbecue asks about the barren ground near their store. The elderly lady explains that the area is a proving ground and her husband adds that the government uses the area to test several weapons, like new strains of bacteria to the weather dominator.

Grunt asks in a suprise voice, “The weather domina -?” And Flint raises his hand in the shape of a ‘C’ and the sign immediately tells Grunt to be silent. A retinal eye scanner is lowered from the ceiling and Flint experiences a small flash of light that stings his eyes. The elderly lady tells her husband, Herb, that the strangers look like good risks so she also explains that when G.I.Joe went under the resistance was rumored to have a headquarters located on the proving ground. Flint backs out of the store and quietly thanks them. Herb then turns to his wife, Martha, and tells her that she talks too much. As the Joes ride away, Herb runs out of the store and tosses the money at the Joes since American dollars are worthless.

Grunt speculates that they were out more than a few hours since the old man’s story sounded like Cobra Commander decisively defeated the Joes. But his teammates laugh at him. Still sticking with his theory, Grunt then reminds him that their government doesn’t have a weather dominator - that the weapon was invented by Destro. Lady Jaye tells the Joes that headquarters is the only place they can find answers they can trust.

Under the cloak of night, the Joes discover a frightening sight. Their base has been permanently closed by the order of Cobra Commander.

Cobra soldiers and a Tele-Viper stand guard and Lady Jaye explains that she simply can’t believe it. As the Joes crawl toward their base, Steeler confesses that he wondered what difference the Joes make, and Flint tells Steeler that he may find out and in the worst possible way.

Lady Jaye throws an incendary javelin into the base and the Cobras quickly mobilize and try to put out the fire. As Cobra agents attempt to put out the fire, the Joes use their combined firepower to cut into a wall on the base and destroy a section of the wall, which collapses onto the Cobras.

Knocking down another door with their lasers, the Joes enter the heavily damaged and rat-filled base and Lady Jaye tells her friends, “Breaks my heart. I don’t even recognize the place.” Flint orders the Cobras to be placed in the brig and Grunt soon explains that the Joes’ communication satellite is not in orbit and that they may be the only Joes left. Grunt leads Flint into the communications room and Clutch explains that he called up the duty roster and fifty Joes are listed, and all but six are listed as missing in action. And of the six remaining Joes, three were lost in the last great war against Cobra.

As Clutch solemnly reads the names of their friends, Steeler covers his face and grieves while Clutch pounds the control panel and demands: “HOW? WHY?” And Flint gravely tells all of the Joes, “One way or another - we are going to get the answers.”

The Joes survey the base for equipment and find an APC and several Sky Hawks, which are covered with dust and cobwebs. Flint orders Grunt to take care of Steeler and to try to repair the computer at headquarters while the Joes do a little reconanisance. As Flint, Airborn and Barbecue drive through a town that is vaguely familiar to Flint, the Joes catch sight of the Cobra Imperial Postal Service before Barbeue smashes the glass cover of a newspaper machine and steals a copy of the Empire Times.

Reading the front page, the Joes learn that Cobra Commander plans to make a State of the Empire speech, however, a police car pulls up behind the Joes and the Dreadnoks climb out of the car wearing uniforms. “I guess law enforcement ain’t what it used to be,” comments Airtight. The Dreadnoks walk to the blue painted G.I.Joe APC with their weapons drawn and tell the passengers to exit the vehicle with their hands up. But the Joes burst out of the APC with Silver Mirage Motorcycles and fly over the Dreadnoks, who pursue in their police cruiser.

Lady Jaye, Footloose and Clutch fly in Sky Hawks and while Clutch patches into the weather satellite, Lady Jaye points out to the Joes that Mount Rushmore has been modified to include the faces of Cobra Commander and Destro. Clutch transmits the images from the weather satellite to the other Joes’ monitors and they see that the Lincoln Memorial has been changed to the Cobra Commander Memorial and that the flags of the United Nations have been replaced with Cobra flags.

Flint, Barbecue and Airtight drive past the Capitol, which has a cobra’s hooded head rather than a dome, and lose the Dreadnoks thanks to a garbage truck that blocks their foes’ path. Barbecue notices that the newspaper’s date is the same as when they left. Since Cobra’s changes to the world couldn’t have been made overnight, Barbucue asks what is going on. Flint can only specualte that if they are not in the future, then they might be in another place - but a HISS tank appears at the end of the alley and forces Flint and the others to dive for cover while the bikes crash into the tank and explode. However, the Joes are captured by the Dreadnoks and learn from them that the Joes’ headquarters was bugged.

While Grunt attempts to fix the computer, Steeler, who is sick due to the bug bite on his neck, runs out of the base and screams that they must have died in the explosion and “gone to the Devil.” Meanwhile, a female Cobra agent, who is watching the events inside the Joes’ base, reports to Baroness that she has found Steeler.

Clutch shares with the Joes another image, a statue of the Baroness that has replaced the Statue of Liberty in New York, and Lady Jaye is convinced that the since the Wasington below them is not their Washington, then the matter transmutor created a gateway and blasted the Joes into a parallel world, where many things are the same while others, like Cobra’s victory, are radically different. Unfortunately, her speech is cut short as she announces that Cobra Rattlers are on an intercept course.