At the Statue of Liberty, some kind of celebration is taking place. But in the skies above, the forces of Cobra appear. Many troops descend from their carrier, and land on and around the statue.

There's nowhere to run, nowhere to hide, and panic spreading far and wide. Who can turn the tide?

"Yoooo Joe!"

The Joes have arrived, and they start to battle against Cobra. But up in the carrier, Destro passes Cobra Commander a time bomb.

Cobra Commander leaves the carrier by using a C.L.A.W., and sets up the bomb on the statue. He then goes to fight Duke, puts gets punched and falls onto a Flight Pod. Meanwhile the other Joes continue with their counter-attack.

"G.I. Joe is the codename for America's daring, highly trained special mission force. Its purpose: to defend human freedom...

...against Cobra, a ruthless terrorist organization determined to rule the world."

Duke fires off some shots and then goes for the bomb. With just 7 seconds left, he grabs it and then uses his jetpack to get to the carrier, planting the bomb on part of it. As he leaves the scene, the bomb explodes...

...and the carrier is destroyed. Cobra Commander tells his forces to retreat, as Duke grabs an American flag and meets up with the other Joes on the top of the Statue of Liberty.

Later, at Cobra's Terror Drome, the true leader of Cobra, Serpentor, curses his own troops. They posses power greater than any other on Earth, but they haven't conquered anything. Their most dangerous enemies is not G.I. Joe, it's the collective incompetence of his own forces! Cobra Commander thinks otherwise -the faults lie with Serpentor and his pompous and pathetic leadership abilities!

Serpentor agrees, saying that leadership is at the very heart of this matter, but the faults aren't with himself -it is Cobra Commander's leadership skills which are the problem. His ego-driven stupidity has converted victory to catastrophe for the last time! Cobra Commander thinks Serpentor is trying to make him into a scapegoat, and says his loyal subordinates would testify to his superb stewardship of Cobra, but Serpentor doesn't have the courage to allow them to speak.

Serpentor tells him he's wrong again, and tells everyone to defend him if they can. Cobra Commander says they shall, and tells Destro to go first. Destro says that militarily speaking, Cobra Commander is a world-class buffoon. Cobra Commander asks the others if they will let Destro's character assassination go unchallenged, and Dr. Mindbender says certainly not.

He steps up and says that Destro forgot to mention Cobra Commander's frequent displays of cowardice. Outside the base, something rises out of the river. A single person called Pythona appears, and makes her way through the bases's perimeter fence.

Back inside, Baroness and the others join in on criticizing Cobra Commander, saying that his idiocy has done nothing other than bring them defeat, again and again. Cobra Commander tells Serpentor that the things they're saying about him are all lies!

An alert then sounds, and the base is put on battle stations. It's an intruder alert, and some Flight Pods are sent out to investigate. They arrive just in time to see Pythona cut into a door, and enter the base.

Pythona encounters some mechanics, which she takes out by using some kind of creature to spray gas into their faces. Destro says their security has been breached, and Cobra Commander thinks it could be as assassination attempt. He wants to leave Serpentor here, whilst they go and intercept the intruder. Serpentor intends to meet the intruder himself, but the others tell him they must protect him, as without him, there is no Cobra.

Cobra Commander agrees, saying that if something happened to Serpentor it would be tragic. He leads everyone out of the room, as Pythona continues to make her way into the base. She uses strange powers...

...and is also capable of releasing acid from her hands. As Cobra Commander's group approach a corner, Cobra Commander sees Pythona running down a corridor.

He deliberately leads his group in the opposite direction. Pythona is able to enter the control room, as the doors around it are sealed. She throws some more gas bombs at the Cobras in the room.

As she approaches Serpentor, he fires several needles at her, which she avoids. He has his throne move downwards.

Pythona defeats Serpentor's guards, and drops down to where he is.

Serpentor says none may challenge him, this he commands. But she says that won't be necessary. Serpentor says he has seen her before.

He has seen her, along with the others...

He tells her he's seen her in a dream, a vision. Pythona introduces herself, and says she's part of his destiny. When he was created, her face was etched into his soul. She tells him it is time for him to fulfill his destiny, and presents him with a clamshell. This clamshell opens up, displaying a hologram of something called the broadcast energy transmitter.

The B.E.T. is currently in the Himalayas, where some Joes are working on it. Mainframe excitedly says everyone will hear about this if it works, as it will pump pure energy through the air. Duke says that is if it works, but Dial-Tone tells him it'll work perfectly, he can practically feel its little semiconductors singing under his fingertips. Scarlett wants to find out if they've wasted a billion taxpayer dollars.

Duke turns the B.E.T. on, and says this could be the key to the world's energy crisis. The B.E.T. starts working, but has an unexpected side-effect -the sudden burst of energy turns on several vehicles.

Cross-Country has to go chasing after his H.A.V.O.C. after it moves off by itself. But he then runs back, as Cobra have arrived! Serpentor tells his force to destroy everything except the broadcast energy transmitter -this he commands!

The Joes are unprepared for this sudden attack, and many of their vehicles are blown up before they can use them. Duke tells everyone to fallback and regroup for a counter-attack. Cobra Commander hopes that this contraption they are going to steal is worth it, as this operation is costing them dearly. Serpentor tells him it is none of his concern. He just needs to do as he's told, like an obedient lackey.

Cobra Commander gets offended, but then his vehicle gets gunned down by Roadblock and Snake Eyes. Duke runs forward to the broadcast energy transmitter.

Serpentor orders for the Dreadnoks to cut Duke down, and they fire on him. But they are then fired on by Quick Kick and Snow Job, and some of them are knocked off their bikes.

Serpentor dives down towards Duke, but he manages to grab onto his chariot and throw a grenade into it. Duke drops off, and the chariot explodes a few seconds later.

Duke goes back to the B.E.T. and turns it back on. The Joe's missile launchers are turned on, and they fire at Cobra.

Many of Cobra's vehicles are destroyed. Serpentor gets back up and starts fighting Duke. Baroness says their emperor needs them, but Cobra Commander says only when he orders it.

Serpentor lands a few punches on Duke, knocking him down. He jumps towards him, but Duke uses his legs to send him flying into the B.E.T.'s dish. Serpentor gets electrocuted.

He falls to the floor, defeated. Baroness sees this and wants to save their leader, but Cobra Commander stops her. He says they must retreat, stating that the Joe's counter-attack is something they need to deal with. He tells everyone to retreat to the mountains, as he knows a place where they can find sanctuary.

Cobra withdraws. Duke says he hates to do this, but he'll have to split up the force. He orders Roadblock to form a unit and go after Cobra. The rest of the Joes will deal with the B.E.T. and Serpentor.

Cobra continues towards the mountains, but Mindbender thinks this is madness -their men are half frozen! Cobra Commander tells everyone to head for the pass up ahead, but they are then attacked by G.I. Joe. Cobra makes it through the pass, and arrive at a strange place.

They don't have time to look at it for long, as G.I. Joe follow them. Quick Kick thinks this looks like something from the Twilight Zone, but Roadblock says to forget it, it's battle time! He charges forward, but then a new enemy appears: Nemesis Enforcer. He takes down Roadblock.

More new warriors jump out of the ground, all armed with large swords. They quickly overpower the Joes.

Snow Job manages to get into a H.A.V.O.C., and starts firing. He then sees Cobra Commander and tries to shoot him, but the H.A.V.O.C. gets stopped in its tracks by Nemesis Enforcer, who uses the blades on his arms to cut into the vehicle.

He tosses Snow Job out. Cobra Commander congratulates his friends, and tells Nemesis Enforcer he's as impressive as ever, but is then struck by him.

Cobra Commander can't believe he did that -Golobulus will have his head for this! Pythona appears, and tells Cobra Commander to worry about his own head. She tells everyone to come with her. Cobra Commander tries to escape, so she orders Nemesis Enforcer to fetch him.

He does so, grabbing Cobra Commander and flying away with him. The Cobra troopers are taken away, and Ripper wants to know where they're being taken to. Pythona, who calls him by name, says he'll find out soon enough. She says they know everything, including the fact that Serpentor has been captured by G.I. Joe. She wants them to rescue him, but they don't like the idea of raiding the Joes at all.

Zartan tells her they don't know who she is, where she comes from or even what side she's on, so why should they risk their necks on her behalf? She reveals a large gem, and asks if it answers their question. Zartan says that a gem of that size answers all of his questions.