In the Gulf of Mexico, a giant tidal wave created from the massive destruction of the Cobra underwater bunker is overtaking the WHALE. It soon reaches the Joe Air-Sea Base and hits it hard. The U.S.S. Flagg also gets hit, causing it to list at an angle. Underwater, the explosion along the fault line is causing a section of sea floor to push up to the surface. The Cobra base inside of the sunken oil tanker rises up with it, and the Cobra troops and vehicles reach the surface of the new island in tact. A Cobra troop carries out a Cobra flag and plants in into the ground.
In Washington, D.C., New York City, Mexico City and Havana, Cobra diplomats work to negotiate for the recognition of Cobra Island as a country. In the gulf, the Air-Sea Base sits at a forty-five degree angle. Everyone is knocked out. Everyone on the WHALE is out as well. The hovercraft comes drifting up to the platform and bonks the side. Shipwreck is amazed that Cutter got them back to the base in his sleep. Shortly after, Duke tells everyone that they have to get Cobra off of the island before the diplomats can do their job.
The Cobra defenses are setting up when the WHALE begins its attack It is almost destroyed by Rattlers. Ace manages to launch a Skystriker off of the listing Flagg. He shows up and takes care of one Rattlers. ASPs on the beach fire at the Skystriker, but miss and hit the second Rattler instead. Ace does get damaged, and must retreat. The Joes land on the beach and began running up the muddy hill. They attack with brutal force and overtake Cobra troops, including Tomax and Xamot. Barbecue jumps onto a HISS tank and takes out the windshield with his axe.
Cobra Commander returns to the Cobra tanker base wounded. The Joes reach the tanker soon after and storm in. Just before they take out the Cobra leaders, Duke receives a call from Hawk at the Pit. He states that Cobra Island has officially been recognized as a sovereign state. All Joes are ordered off of the island. The Cobras are thrilled to the point of laughing. The Joes are furious to the point of silence.
The Joes have returned from their battle on Cobra Island. Rip Cord is being taken to the hospital to recover from his injuries. He is informed that the Dreadnok Buzzer, who just escaped from the The Pit, has kidnapped his girl friend Candy and is on the loose.
General Austin is talking to Hawk about the Cobra Island debacle when he has a heart attack. Now, Hawk must go to Washington DC and he is going to take Stalker and Snake-Eyes with him.
The Soft Master catches a ride into Springfield with a traveling salesmen named Chuck. Chuck drops him at the police station. The Soft Master leaves his suitcase in the car, as Chuck drives off. He then enters the police station to ask the officers to look up a name in their database.
Billy, Cobra Commander's son, continues to receive ninja training from Storm Shadow, he has become Storm Shadow's apprentice.
Near the GI Joe base Fort Wadsworth, Fred Broca (Wade Collins) leaves his Cobra planted family, including his son Sean, to trail Hawk as he leaves the base for Washington DC.
Buzzer and Candy are on the outskirts of Springfield. Buzzer is planning on giving the location of the GI Joe headquarters to Cobra. He has been fighting with Candy the entire trip. After Candy is able get a hold of a gun, she kicks Buzzer out on the side of the road and leaves him behind.
Billy has learned many ninja training techniques from Storm Shadow. But as Storm Shadow talks about his past, especially the death of the Hard Master and his mysterious killer, Billy makes a decision. His decision is to confront his father about many things including who killed the Hard Master. The Hard Master is the Soft Master's brother and Storm Shadow's uncle. So he leaves his training and Storm Shadow to go to Springfield to find his father.
At the police station in Springfield, the Soft Master has taken out all of the officers. And now has gained access to their computer system where he will be able to get a print out of all the information pertaining to the Hard Master.
After dropping off Hawk at General Austin's hospital, Snake-Eyes and Stalker head to the Vietnam Memorial to pay their respects to their fallen comrades. Back in Vietnam, Stalker, Snake-Eyes, Storm Shadow, Ramon Escobedo, Dickie Saperstein and Wade Collins where on a long range recon patrol, when they walked into an ambush, only Stalker, Snake-Eyes and Storm Shadow walked out alive. They are there to look up Ramon, Dickie and Wade's names. When they get to the spot in the directory where Wade Collins name is supposed to be, it is not there. Fred Broca, who is actually Wade Collins Cobra Crimson Guard agent, reveals to them that he is very much alive and holds them at gun point.
Wade Collins (Fred Broca) is holding Snake-Eyes and Stalker at gun point near the Vietnam Memorial. They had thought that Collins had died in Vietnam. They were all on an LRRP (Long Range Recon Patrol) back in the Nam. Collins then goes on to tell the story of that patrol.
The LRRP included Snake-Eyes, Tommy Arashikage (Storm Shadow), Lonzo Wilkinson (Stalker), Wade Collins (Fred Broca), Dickie Saperstein and Ramon Escobedo. Collins was on point when he walked into a bivouac of a full company of NVA regulars. Collins was hit several times in the chest with bullets. Next to him Escobedo is also hit several times. Stalker checks to see that Escobedo is dead, and leaves Collins assuming he is dead. As Saperstein is flanking the NVA's, he steps on a mine that completely blows him apart. Storm Shadow, Snake-Eyes and Stalker are then forced to retreat leaving the almost dead Collins to the NVA's. After the NVA's fixed him up, he sat in a POW prison camp for months, finally to be released when the war was over. After returning to the US, he was spit on for being a soldier, divorced by his wife and unable to get a job. He then discovered Cobra, where he was able to gain power, respect and friends. Once inside Cobra, the Crimson Guard, the Elite soldiers of Cobra, was formed and Collins was one the first to join. It required plastic surgery to become one of the Fred Broca series. Later, he was sent to replace another Fred who had died. He took over that family that was stationed right outside Fort Wadsworth to watch for GI Joe's, which is how he came to be standing in front of Snake-Eyes and Stalker.
Stalker is able to convince Wade that his current life filled with hatred and bitterness and dedicated to a totally corrupt organization like Cobra has made is life worse. They all return to Collins' "family" home where is he has planned to leave Cobra. As he is telling them about leaving, his son, Sean Collins, makes a decision to stay with him, and the rest of the family follows along with him leaving Cobra. Stalker and Snake-Eyes wish them good bye and good luck as they drive off.
Meanwhile, another part of Snake-Eyes' life is playing out in Springfield.
The Soft Master has just assaulted an entire police station to discover the Hard Master's killer. He uses the last officer standing to gain access to the computer system. After doing some searching he is able to find the information that he is looking for but doesn't reveal it. Additional, police support shows up causing him to make his escape.
Buzzer, after being dumped on the side of the road by Candy, has arrived in Springfield and is met by Firefly and Scrap Iron.
Billy, Cobra Commander's son and Storm Shadow's apprentice, has also arrived in Springfield.
Chuck, the same man that gave a ride to the Soft Master earlier, has now picked up Candy. Candy discovers the Soft Master's suitcase in Chuck's car. So they turn around and head back into Springfield to return the suitcase. On the return trip, they pick up another hitchhiker, Billy, who upon getting in the car, senses death.
The Soft Master has stolen a police car and is racing out of Springfield. With Firefly, Scrap Iron and Buzzer hot on his tale he just beats a train but in the process crashes into Chuck's car. Inside the car, Chuck, Candy and Billy are all injured. The Soft Master turns around to check on the people in the car. Since the train has divided the accident from Firefly. He orders Scrap Iron to climb the telephone pole and see what is happening on the other side of the train.
Scrap Iron sees the Soft Master helping the people in the crashed car and fires a missile at him. The Soft Master sacrifices himself my jumping into the on coming missile. Scrap Iron then asks Firefly what he should do with the rest of the people in the car. Firefly gives the thumb down symbol and Scrap Iron fires a missile into the car killing Candy, Chuck and apparently Billy.
As Lady Jaye leads some new Joe recruits on a training mission, they are attacked by strange robots running at them with strange canisters on there backs. These robots, actually B.A.T.S. (Battle Android Troopers), where created by Dr. Mindbender and release the creeper bomb, vine like organism that strangles the vehicles, releases a sleeping gas that knocks out all the Joes.
The new recruits, Bazooka, Crank-Case, Heavy Metal and Airtight along with Lady Jaye, wake up in a junkyard that is a maze of trashed cars. This is actually a test set up by Dr. Mindbender to promote his BATS and creeper bomb to Destro and the Baroness, so that he can sell them to Cobra.
The Joe vehicles, the MBT Mauler tank, Silver Mirage motorcycle and AWE Striker have been stripped of all their ammo and the only weapons the Joes have. As they are chased by BATS driving HISS tanks and motorcycles all carrying the creeper bombs. Many of the BATS are destroyed; Airtight is able to figure out a way with car battery acid to defeat the creeper bombs and there sleeping spores. The test isn't going very well for Dr. Mindbender.
Finally, Destro and Dr. Mindbender are attacked directly by the Joes, and the Baroness swoops in on a Fang to rescue them just before the creepers get them.
After defeating Cobra, Lady Jaye gives all the new recruits a passing with flying colors rating.
As Ace and Rip Cord fly over Cobra Island on a recon mission, Rip Cord ejects to go on personel mission to find his girlfriend, Candy. Candy had been captured by the Dreadnok Buzzer and has disappeared; actually she was killed by Scrap Iron in Springfield. Cobra Commander keeps any information about her status from Professor Appel, her father.
In The Pit, new Joes Alpine and Quick Kick are staging for mission with Spirit, Flint and Snake-Eyes. Their mission is to help support and rescue Rip Cord, also is gather information about the new island, and the new hardware that Cobra has on display for the satellites to see.
As they are waiting, a message comes in specially marked for Snake-Eyes, he reads the message and rushes out of the base.
In the US Army Medical Center in Washington DC, General Austin is briefing Colonel Hawk on the information about Cobra Island. He gets the President of the US, as well as the Joint Chiefs chairman to confirm that Colonel Hawk is promoted to Brigadier General and commander in chief of the GI Joe team. General Austin is retiring. Hawk receives his stars.
Snake-Eyes invades Storm Shadows New York lair, where he gives him the message that came from the Soft Master, revealing the Hard Master's killer to be Zartan. Zartan used a compound bow with sound amplifaction-directionl-ranging equipment to pick out the man he thought was Snake-Eyes. The Hard Master had been doing the "Cloak of the Chameleon" technique and was imitating Snake-Eyes when Zartan fired his arrow. Storm Shadow swears revenge, he and Snake-Eyes take off for Cobra Island to find Zartan and kill him.
Flint's team is launched from a plane for a beach incursion to find Rip Cord.
Meanwhile on Cobra Island, Rip Cord has made his way toward Cobra's main base, but Zartan has taken out his old bow in order to take out Rip Cord. As they fight, Rip Cord gets shot in left arm by an arrow, and Zartan shot in right shoulder by a bullet. Then Zartan uses his special abilities to hide himself and sneak up on Rip Cord, who actually tricks Zartan. Then they get in a wrestling match, and apparently Rip Cord comes up the winner, but actually it is Zartan; he has taken on Rip Cord's identity.
Snake-Eyes and Storm Shadow have discovered that Zartan is the killer of the Hard Master, and they have come to Cobra Island to kill him.
Flint's team, Spirit, Alpine and Quick Kick, have also come to Cobra Island in order to rescue Rip Cord, and do some additional recon of Cobra Island. Back at The Pit, Hawk has gather the Joe team for a full out invasion.
Zartan has taken on Rip Cord's identity, using his powers of transformation plus he adds Rip Cord's original uniform to help with the transformation. His plans are be discovered by Flint's team and taken back to Joe headquarters. He leaves the alive but very beaten Rip Cord dressed in his own uniform.
Professor Appel, whose daughter is Candy, Rip Cord's girlfriend and the reason he is on the island, shows off the Cobra firebat to Cobra Commander. The Commander still doesn't have any information about Candy's location, so he gives the Professor the run around about why his daughter can't come to the Island.
A little later, Professor Appel is doing a recon of the island, he comes upon Rip Cord dressed as Zartan and takes him back into the Terror-Drome. As he is inspecting him, he discovers that Rip Cord is holding a picture of his daughter. He realizes that it is the real Rip Cord disguised as Zartan that he has in custody. Appel figures out that Cobra Commander has been lying to him about his daughter. He decides on the spot to help Rip Cord. So in order to prevent any Cobras from discovering Rip Cord dressed as Zartan he hides him in the firebat and begins the preparation to launch.
Storm Shadow and Snake-Eyes wreak havoc on Cobra Island as their search for Zartan. From the control tower in which they have just conquered, they see Professor Appel pick up Rip Cord dressed as Zartan, and of course they now know where he is and set off toward the Terror-Drome.
Flint's team spots Zartan posing as Rip Cord just as a Cobra patrol is about to attack him. They give him some support, and since Zartan isn't aware of who is firing, he blends into the sand, causing Flint to doubt himself. Eventually, they find Zartan, and begin to make there escape from Cobra Island.
Tomax and Xamot organize some serious resistance to the dynamic duo, once they have entered the Terror-Drome. Snake-Eyes and Storm Shadow are just too powerful for the regular soldiers of Cobra and they defeat everybody that gets in there way. They reach Cobra Commander, who quickly gives up the information on wear Zartan is, plus he lies about ordering Zartan to kill the Hard Master and adds a comment about how Zartan did it just to prove he could.
As Rip Cord dressed as Zartan sits in the firebat, Professor Appel has reached the final stages of the launch. Storm Shadow busts in killing Professor Appel before he can say anything about the Rip Cord/Zartan switch. Fortunately for Rip Cord, Appel was able to hit the launch button before dying. Storm Shadow makes an attempt to kill Rip Cord inside the firebat as it is taking off, but Snake-Eyes stops him, saving Storm Shadow's life. Zartan has gotten away.
Out on the ocean, Spirit is inspecting the real Zartan posing as Rip Cord, and notices several discrepancies from Zartan's real wounds and the wounds of the uniform that he is wearing.
Zartan posing as Rip Cord is loaded onto the Whale. Doc, along with several other Joes, is there to help with the extraction of Flint's team who recovered Rip Cord/Zartan.
Overhead in a firebat leaving Cobra Island on pre-programmed course is the real Rip Cord, who is dressed as Zartan.
Incoming to Cobra Island is Destro, Dr. Mindbender, the Baroness and Buzzer in a helicopter that is damaged by the Whale's missiles.
And on Cobra Island, Snake-Eyes and Storm Shadow are fighting desperately to find a way off the island. They head for the airfield, and just as they arrive, the helicopter that Destro is in crashes into several planes and blocks the runway. There next option is the docks to find a boat.
On the Whale, Doc is treating Zartan, when he gives him an injection Zartan briefly reveals his true self to Doc, who doesn't believe his eyes and reports to Hawk that something isn't right about Rip Cord. But it is too late; Rip Cord is loaded up to a Dragonfly for fast extraction.
Ace drops off two Devilfish, fast attack boats, to help support the mission. Hawk, using the Devilfish, personally leads a mission to rescue Snake-Eyes on the island with Beach Head and Wet Suit as his support.
Snake-Eyes and Storm Shadow have been able to steal a Cobra Hydro-Foil, Snake-Eyes mans the turret as Storm Shadow drives. Dr. Mindbender leads an attack on the Hydro-Foil with his new super fast torpedo transports. One of his torpedoes hits the ski of Hydro-Foil making it impossible to control, at the same time two Eels attack Storm Shadow. The Hydro Foil crashes into the island causing Storm Shadow and the two Eels he is fighting to fall into the sea.
Hawk and the two Devilfish enter the battle, one Devilfish is destroyed, and the other is able overturn Dr. Mindbender on his sled. As Beach Head, Wet Suit and Hawk approach the destroyed Hydro Foil they see a shark frenzy starting near where Storm Shadow is located. They are able to speed in and grab Snake-Eyes and get out before the sharks get them.
Wet Suit spots Storm Shadow walk out of the surf on the beach, alive. The Baroness pulls up and just shoots Storm Shadow saying "You've betrayed Cobra once to often and I intend that you never betray us again." Snake Eyes watches on helplessly.
In Springfield, the Firebat carrying the unconscious Rip Cord lands on the runway. Ripper, Torch and Firefly are there to meet him and take him to a Cobra hospital.
In New York, the unconscious Zartan is taken from a C-130 directly to The Pit.
On Cobra Island, Destro, the Baroness and Dr. Mindbender inspect the dead body of Storm Shadow. The Baroness reminds them that a ninja is able to slow there respiration and heartbeat. Dr. Mindbender orders the body taken to cold storage.
In The Pit, Doc is taking a blood sample from Zartan who is still posing as Rip Cord. When Doc returns Snake-Eyes/Zartan is in room and he knocks out Doc. Scarlett sounds the alert that an intruder is trying to escape. All Joes are on alert. A cat and mouse game happens as Zartan continues to change into different Joes and causing lots of confusion and mistaken identity. In the communication room, Zartan/Doc is grabbed by the Joes, just as the real Doc enters the room. Breaker has just received a message from Rip Cord that Zartan has taken his place and is in The Pit. Zartan turns invisible, which is just a camouflage trick, but it works and gets him free in the Pit, again. Another part of Breaker's message is that Rip Cord also knows the location of Cobra headquarters.
In Springfield, Buzzer tells Rip Cord, who is dressed as Zartan, that he escaped from The Pit with a girl prisoner. Rip Cord demands to know about the girl. That girl is Candy, his girlfriend, who is now dead. The last Buzzer saw of her was when she kicked him out the car. Rip Cord attacks Buzzer. The Dreadnoks subdue Rip Cord/Zartan and take him out of Springfield. At a rest stop, Rip Cord is able to call The Pit and inform them about the switch Zartan made back on Cobra Island and that he knows the location of Cobra's headquarters.
Back at The Pit, Sgt. Slaughter has just arrived.
Zartan makes his way to the surface with Gung-Ho right on his heals. Zartan/Gung-Ho starts fighting Gung-Ho when Sgt. Slaughter comes up to the fight. Sgt. Slaughter just hauls off and knocks Zartan out cold. When asked how he knew there right one to hit, "The odds were fifty-fifty. Guess, I was lucky."
At a diplomatic meeting in Washington DC, a Cobra diplomat is negotiating official relations with the US government. And Hawk has his first meeting with the group called the Jugglers. They give Hawk his first order, Cobra Island is completely off limits to GI Joe.
At the Springfield Museum, Destro & Dr. Mindbender collected 10 of the world's greatest leader's remains. These remains DNA will be scanned by the Brainwave Scanner in order to create the ultimate soldier. The combination of these leaders' DNA, mixed in with Storm Shadow's as well, will be fed into a simulacrum body. Then Dr. Mindbender will add his own modern technology knowledge and allegiance to Cobra into the Scanner mix. The Scanner will then combine them all together to make a great Cobra leader called Serpentor.
At a bar in Springfield, Rip Cord dressed as Zartan along with the Dreadnoks are partying it up. Unknown to the Dreadnoks is that Rip Cord has just given up the location of Cobra Headquarters to GI Joe. Firefly and Scrap Iron break in because they intercepted the call to Joe headquarters. Rip Cord's cover is blown and he is captured by Firefly. The Dreadnok and Firefly then drag Rip Cord to the Brainwave Scanner over at the museum to see exactly what he told the Joes. On the scanner monitor, they watch Rip Cord give the coordinates of Springfield to Breaker. Cobra Commander immediately orders Destro to evacuate Springfield.
By connecting Rip Cord to the Scanner, unknowingly his GI Joe knowledge is also combined into the Serpentor mix. And Serpentor has now been created.
Hawk assembles all of the Joe team, some of the Joes with desk status are temporary upgraded, and many new members are going to get there first taste of fighting Cobra. The plan: the Strike team, lead by Hawk, will secure the airport and then move to neutralize the main headquarters. The Security team, lead by Duke, also helps with taking the airport and then moves to block the roads heading out of town. The Assault team, lead by Stalker, goes in early to cut off the power and communications. Additional, air support will come from Wild Bill and the new helicopter pilot Lift Ticket.
The Assault team goes in first and is successful in taking out Springfield's power and then moves on to secure the police station. The other teams are successful in taking the airport, and GI Joe has begun it invasion of Springfield.
At the museum, Serpentor has taken command of the Cobra ground forces that are left in Springfield. His mission is to lead a holding action against both the Strike and the Assault teams of GI Joe, allowing Cobra enough time to evacuate the city. The Baroness is handling the evacuation of Springfield with support from Destro. Because Serpentor is an unknown quantity, Firefly is given the assignment of watching him and to kill him, if he acts against Cobra.
The Battle of Springfield:
The Assault team has run into the main Cobra forces lead by Serpentor, which is headed to the airport. Recondo and Scarlett are injured, and the team is pinned down. The newly created Serpentor has taken command of the Cobra forces. He is leading his troops from the front lines. Not leaving any soldiers behind and even ignoring a bullet wound. Stalker, leader of the Assault team, warns Hawk, leader of the Strike team stationed at the Airport, that the Cobra forces are coming there way and his team can't do much to stop them.
The Security team, lead by Duke, has just finished securing the exits points of the city, preventing any major evacuation of Cobra by road.
On the other side of town at the Springfield High School, the full blown evacuation is taking place. Destro and the Baroness are leading the well planned escape. Cobra agents have destroyed all Cobra documents and paraphernalia before evacuating to the high school. At the high school, they are loaded into the cargo helicopters from the football field and head to their new home on Cobra Island.
Back in the main part of the city, Serpentor along with Firefly and Dr. Mindbender, are fast on the heels of Assault team headed in the direction of the airport. Duke, with the Security team arrives at the airport to help secure and defend it. Hawk has taken his Strike team to where he thinks the Cobra headquarters is located, the Springfield Museum.
Inside the museum, the Dreadnoks are the only ones left. Rip Cord is still connected to the Brainwave Scanner. The body of Storm Shadow is still in one of the containers that helped to create Serpentor.
At the football field, Baroness tempts Destro with taking over Cobra and he should leave Serpentor behind. Destro, a man of honor, makes a plan to help Serpentor and his troops escape with the rest of Cobra.
The presumed dead Storm Shadow wakes up just as Ripper is about to steal his sword. Storm Shadow has been revived by the Serpentor's creation process. He had put himself in a ninja trance called The Sleeping Pheonix that had slowed his breathing and heartbeat to near death levels. He is very confused as to where he is but very alive, he escapes with the Dreadnoks out the back door just as the Strike team attacks. Once inside Hawk realizes that the place as been abandoned. They are able to rescue Rip Cord, who tells them about how the place is set to blow up.
Over at the airport, Zap has just discovered an underground tunnel system, which was used to move all of the cargo helicopters to the football field for the evacuation. The entire tunnel system is then blown up. Cobra has just faked out the Joe team.
The Assault team arrives at the airport. Serpentor and his tanks charge at the team, which are promptly destroyed. The forward assault was a cover that allowed Destro to come in during the destruction of the tanks and rescue Serpentor and all his men. But Serpentor gives the Baroness all the credit for his liberation.
On Cobra Island, Cobra Commander has been getting constant updates on the successful evacuation of Springfield and Serpentor. He realizes that he can't let Serpentor land on Cobra Island.
The Joes have just destroyed a town, with very little proof of Cobra to show for the action. Standing at the airport, Hawk receives a call from the Committee of Generals at the Pentagon, the Jugglers.
A few hours later in New Jersey, Storm Shadow and the Dreadnoks arrive at their hide out, where they run into Zarana, Zartan's sister.
Best Defense:
A flight leaving San Francisco has been hijacked. The 3 man terrorist team, called the Leon Trotsky Brigade of the Fourth International, is planning on flying the plane to Russia. On the plane, Roger has C-4 strapped to his chest and is holding a "dead man's stick". A dead man's stick is a button that is held down and when released the bomb explodes. Meryl is controlling the passengers in the cabin and Wesson is in cockpit with the pilots. The Joe team of Beach Head, Hawk, Flint, Lade Jaye and Stalker are investigating at the airport. A report comes in about a SWAT operation at Fourth International's headquarters in the Mission District. Hawk and Stalker head to the headquarters and Flint, Beach Head and Lade Jaye hop a quick flight to the refueling airport in Anchorage, Alaska where the captured plane is flying.
At the headquarters, Stalker and Hawk charge right into the fight. Stalker has brought a Taser in order to capture one alive. Hawk makes a quick distracting action that the terrorist falls for and Stalker steps in with the Taser, knocking her out.
In Anchorage, the plane has landed and is refueling. Beach Head, Lade Jaye and Flint sneak onto the plane through the wheel wells and the plane takes off again. Once inside, they cut holes in the floor to sneak into the main compartment. Lade Jaye changes into a stewardess outfit, Beach Head hides near the back of the plane and Flint gains access from the toilet which is near the cockpit.
As the plane approaches Russia, MiG airplanes are threatening to shoot down the airliner if it enters Russian airspace.
Hawk has gotten the plan out of the terrorist Stalker captured. They are planning on crashing the plane into a Soviet chemical warfare depot. The Joe team on the plane goes into action. Beach Head takes out Meryl, as Lady Jaye confronts Roger and his bomb. She hits him with a Taser, grabs the "dead man's stick", opens the escape hatch door and throws him out. Flint takes out Wesson who is in the cockpit. All just as the plane is about to enter Russian airspace. The MiG's have authorization to fire but the Joe controlled plane turns just before entering Russia's airspace. All the passengers are safe.
In New Jersey, Storm Shadow and the Dreadnoks, Buzzer, Ripper and Torch, have just fled the destruction of Springfield. At the hide out they meet Zarana, Zartan's sister, also there is Zandar, Zartan's brother, as well as a new Dreadnok Thrasher.
Zartan has been a GI Joe captive for quite a while, and Buzzer has known the location of The Pit, GI Joe's secret base, for even longer. Zarana is going to bust him out and she will use a disguise to do it. Additionally, she has just gained, from an intercepted Federal courier, some of the secret dossiers of the GI Joe team members.
Using the identity of Lady Jaye, Zarana, along with Zandar posing as interrogation specialist, drives into The Pit. In the lower levels, Sgt. Slaughter releases Zartan to them so they can interrogate him. Now dressed as Scarlett, Sgt. Slaughter and the specialist, they begin to make their way out of the The Pit. Plus, they are able to steal a super secret com-link module that is programmed to all the Joe radio signals.
Over at McGuire Air Force base, most of the Joe team has just returned from their invasion of Springfield. Cross Country arrives at The Pit just as Zarana is leaving and figures out her disguise. He had just seen the injured Scarlett over at the airbase. But they are still able to escape. Moments later after calling Hawk with the escape news, Sgt. Slaughter jumps on the HAVOC and takes off after them.
When Zarana is driving out, Storm Shadow sneaks out into the elevator shaft of The Pit. Over at McGuire, Hawk takes off to a meeting in Washington.
Hawk sends Crank-Case, Alpine and Flint in Awe Striker with Roadblock, Shipwreck and Heavy Metal in the Mauler to intercept Zartan.
After meeting up with the rest of the Dreadnoks and the Thunder Machine, they head into the swamps, where an ambush by Flint's team is waiting. The Joes get the drop on Zarana and Zandar, but then Thrasher's Thunder Machine tears apart the Mauler and knocks over the AWE Striker. Zartan and his siblings think they are free and clear when Sgt. Slaughter shows up in the HAVOC.
A running and gunning battle happens between the two machines, each causing partial damage to the other but neither stops fighting. The Thunder Machine is able to dodge in front of an on-coming train before the HAVOC can make it across the tracks. Sgt. Slaughter tries to follow in the utility flyer. He approaches a gas station with an attendant sitting outside and asks if he saw any unusual people pass by. "Yep, the fellers you want went tooling down that road over there." Sgt. Slaughter thanks him and takes off down the road. The attendant is Zandar and the gas station is the Dreadnok hide out.
Immediately after the evacuation of Springfield, Serpentor is making his first appearance on Cobra Island. Cobra Commander has sniper teams ready to kill him; on purpose Serpentor gets really close to the Commander, preventing any clear shot. He then proceeds to give a grand speech, as Cobra Commander stays silent. Serpentor has now become the popular choice in the Cobra organization.
Destro, Baroness, Dr. Mindbender, Tomax and Xamot are all in the middle trying to avoid picking sides. But early on the Baroness is siding with Serpentor, and Tomax and Xamot on Cobra Commander's side.
In The Pit, some of the Joes including Quick Kick, Stalker, Scarlett and Snake-Eyes are practice there martial arts when Storm Shadow jumps down from the ceiling, much to everyone's surprise. He is asking to speak to Snake-Eyes. After dispatching several Joes including Stalker, he comes to Scarlett. As they stand face to face, Storm Shadow understands that she loves him, and knows Snake-Eyes' heart. She is allowed to stay as he talks to Snake-Eyes.
Back on Cobra Island, Serpentor is easily winning over all of the troop's right in front Cobra Commander, and there isn't much he can do about it until Zartan calls. Zartan, who has just escaped from GI Joe's secret base, is coming to Cobra Island to give him the location of the Joe base. Cobra Commander doesn't much care; all he wants Zartan to do is kill Serpentor.
In Washington DC, Hawk has just come from a meeting with bad news. The fact that Zartan knows the location of the base isn't the bad news.
Cobra Commander's plan is have Zartan, along Zarana, Zandar and the Dreadnoks kill Serpentor. So an attack is staged. Zartan and the Dreadnoks are all dressed as Joes, specifically Flint, Stalker, Lady Jaye, Snow Job, Rock 'n' Roll, Torpedo and Shipwreck. The Baroness throws herself in front of Serpentor to save his life. The assassination attempt, which Serpentor completely knew was coming, is a failure because Destro ambushes them. A side note is that Destro really saved the Baroness more then Serpentor, and he knows it. Serpentor is able to turn the "failed GI Joe attack" on him to his advantage. Using Zartan & Zarana's knowledge, he is going stage an attack on the GI Joe base. And Cobra Commander will lead it.
Meanwhile at The Pit, Storm Shadow explains how he avoided death. Storm Shadow had put himself in the Sleeping Phoenix, a trance in which the breathing and heartbeat are at near death levels, just as the Baroness was shooting him. His wounds although deadly weren't immediate. His body was then put in stasis, and then mixed in with the Serpentor creation process. All of the experiences of the famous leaders of the past that were funneled into Serpentor went through Storm Shadow, not only healing his body but opening his eyes to how consumed he had become with revenge for the death of his uncle, The Hard Master. He asks Snake-Eyes for a safe haven to restore his health, and soul. Snake-Eyes gives him his keys to the trapdoor to his former cabin up in the High Sierras.
Later, when Storm Shadow finds the trapdoor Timber, Snake-Eyes' wolf, shows up to give him some welcome company.
Hawk gives the bad news; the Joes are suspended until a proper investigation into the invasion of Springfield can be done.
General Hollingsworth, General Ryan and Admiral Dyson are doing an inspection of The Pit and Hawk is escorting them. The Joe team is officially suspended after the invasion and destruction of Springfield and most of the Joes have left the base, a few are still stationed above in the Chaplain's Assistant School.
On Cobra Island, Serpentor has hatched a plan to attack GI Joe's base. This plan manipulates Cobra Commander into directly leading the attack hoping that it will remove him from the Cobra leadership picture.
Flint and Lade Jaye are talking along the waterfront. Flint is actually trying to get her to go on a date with him, when a squad of Eels comes up out of the water. Flint charges the squad by himself, as Lady Jaye runs to warn the last remaining Joes of the invasion.
Meanwhile in the motor pool, which is the part that allows access to the secret lower levels of The Pit, Spirit, Quick Kick, Cross Country and Gung Ho are watching Serpentor, Cobra Commander, Destro, Zartan and Zarana unload a truck full of BATS.
Inside The Pit, Hawk, Gen. Hollingsworth, Admiral Dyson and General Ryan watch Serpentor launch the attack from screens down in the communication center. They raid a weapons locker filled machine guns, LAW's, grenades, satchel charges, and claymore mines. The BATs are in need of leadership. And Serpentor suggests that Cobra Commander lead the attack personally, and Destro volunteers to support him. So Cobra Commander and Destro lead a group of vipers into lower levels of The Pit chasing Hawk.
A heavy fire fight erupts, many of the BATs are destroyed and the vipers are needed to back them up. A BAT covered in high explosives walks toward the Joe team, Admiral Dyson makes a sacrificial attack on the BAT giving the Hollingsworth, Ryan and Hawk time to escape behind a blast door before it explodes killing Dyson.
Above ground, the remaining Joes have opened a battle with the above ground soldiers now lead by Serpentor.
Back below ground, General Ryan has set up explosives along the main support columns. They are going to sacrifice The Pit in order to kill Cobra Commander and Destro. As Cobra continues the attack, a large wall section falls on Ryan, who is now trapped, he then detonates the explosives as Hawk and Hollingsworth enter the escape tunnel.
All of the levels of The Pit collapse, completely destroying it trapping Cobra Commander and Destro in the very bottom level. Serpentor then leads a quick escape.
Moments later, Hawk and Hollingsworth are standing over the ruined Pit morning the loss of Admiral Dyson and General Ryan. The Joes are officially off suspension, and will now be a nomad unit.
On Cobra Island, envoys from the provisional military government of Sierra Gordo are meeting with Serpentor. They are looking for an air defense system to help protect their new dictatorship.
Serpentor unveils a scale model of the Terror Drome, a pre-fab launch base for the Firebat air defense system that costs $250 million US dollars. Within the week they can have it up and running. He also puts Zartan and Zarana in charge of Terror Drome sales.
At Fort Wadsworth, former home of GI Joe, the new fighter pilot Slip Stream is reporting for duty. Below ground in the collapsed part of the former base called The Pit. Cobra Commander and Destro are alive.
In Sierra Gordo, Cobra has just finished assembling the Terror Drome. And the Joes have satellites photos but no idea what it is. Hawk sets up a mission where Snake-Eyes disguised as Flint will get captured and brought into the Terror Drome in order to recon what it is about.
The X-30 Conquest airplane, piloted by Slip Stream, makes its attack with Snake-Eyes in the back seat. The Firebat of the Terror Drome is launched in order to repel the Joe attack. A serious air battle takes place between the Conquest and the Firebat. The Conquest is hit by the Firebat's machine gun and Snake-Eyes ejects landing near the Terror Drome. Tomax and Xamot are easily able to capture him. Snake-Eyes, wearing a mask that looks like Flint, is brought into the Terror Drome put into the old but improved brainwave scanner.
In the very bottom of the collapsed Pit, Destro and Cobra Commander are trying to figure out how to escape. They find the escape tunnel that Hawk was able to use, but it is blocked by rubble. After further exploration, they discover an earth boring escape-vehicle.
Above ground, Grunt, one of the original 13 GI Joe team members, is retiring from the service and headed to school at Georgia Tech.
In Sierra Gordo, Snake-Eyes, disguised as Flint, is connected to the brainwave scanner, which isn't working because he blocks all attempts to get information. Outside, the Joe team, lead by Stalker with Beach Head, Low Light and Leatherneck, are working with Sierra Gordo's counter revolutionaries to attack Cobra and the Terror Drome. As the battle continues, Low Light is able to take out several Cobra vipers. They steal the vipers' uniforms and sneak into the Terror Drome to rescue Snake-Eyes.
On Cobra Island, Serpentor unveils the Cobra Consulate Building. This new base of operations, based in New York City, will be 50 stories of surveillance gear, office space, satellite communications and all under complete diplomatic immunity.
In a mall on Staten Island, Cobra Commander and Destro have escaped from the destroyed Pit. Using a clothing store, they ditch their costumes and disguise themselves with beards and other accessories. Destro sees Cobra Commander's real face for the first time. A little later, the Commander's former profession as a used car salesmen, helps him get a legit Corvette. And they drive off.
Dr. Mindbender figures out that Flint is wearing a mask, so he rips off the mask to reveal Snake-Eyes' damaged face. The Baroness is also present at his unmasking. As the counter revolutionaries get closer, Dr. Mindbender leaves Snake-Eyes alone. Stalker and the rest of his team, dressed as vipers rescue Snake-Eyes. As the team is leaving the Terror Drome, Stalker is shot in the chest, slowing down the group as they are trying to escape with their injured leader. In order to save his old Vietnam buddy, Snake-Eyes sends them all on to the extraction point without him. He chooses to stay behind to hold off Cobra.
Cobra Commander has been pulled over by a regular police officer. After the Commander gives out his real driver's license with his real name on it, the officer recognizes the unusual last name, and seeing a familiarity with his face puts it together who he is. The officer tells a story of a mysterious car accident where everyone died but a young kid named Billy. He was able to crawl out of the wreckage missing a leg, an eye, 3rd degree burns, cracked ribs, cracked skull and he has been in a coma for over a year. The only identification was a name card giving his name and photo of his father, Cobra Commander.
Destro and Cobra Commander visit Billy in his hospital room. Cobra Commander feels terrible for being a bad father, and pledges to stand by him, love him and hopes for forgiveness. Destro leaves Cobra Commander with this comment, "You can't change the past. Let it go. Do something about the future."
In Sierra Gordo, Snake-Eyes has been captured again by Cobra. The attack on the Cobra Terror Drome by counter revolutionaries is forcing Cobra to evacuate. Dr. Mindbender has the brainwave scanner packed up in the firebat, and has Snake-Eyes put in a helicopter to be taken to the new Cobra Consulate Building in New York City. As the GI Joe reinforcements arrive, including Scarlett, the Cobra defenses completely fall apart, and they are able capture an intact Terror Drome.
Serpentor, on his way to Sierra Gordo, is planning on leading a counter attack to take back the Terror Drome but is too late. The Joes have already begun to investigate the Terror Drome. Tripwire has placed charges that cause the Terror Drome to fall apart in sections that can be transported out for further investigation. Tomax and Xamot have stayed behind watching the Joes. So a plan is hatched to divert Cobra. They are going to load some of the parts of the Terror Drome onto a train and take them away. The train is a diversion; in fact the most of the important parts will be taken away by boat. Serpentor falls for the diversion and Cobra chases after the train. GI Joe is free and clear to take the captured Cobra Terror Drome away to the USS Flagg.
Back in America at Georgia Tech University, Grunt is exercising at the football field. He is approached by a girl named Lola. She is former military, actually a helicopter mechanic; Grunt lies about his military experience saying he just worked in the Chaplains' Assistant Motor Pool at Fort Wadsworth. They go off to have lunch.
At Kennedy Airport in New York City, Destro, still in disguise, gets on a plane headed home, his destination Glasgow, Scotland.
On the USS Flagg, Hawk has received information about a man who passed through security at Kennedy Airport with a silver mask. That man was Destro who is heading home to Glasgow, Scotland.
Hawk consults Lady Jaye and Flint about M.A.R.S. (Military Armaments Research Syndicate), Destro's family company. Flint responses with some history of the company; M.A.R.S. an international weapons firm that was originally established in 1752 as naval gun foundry by James McCullen Destro, ancestor of Destro.
Destro arrives at Castle Destro. Much to his surprise, there is meeting going on without him, the surprises continue as an imposter is already sitting in his place, and the imposter has the real Destro arrested and taken away to jail.
Flint and Lady Jaye arrive in Scotland, and are met by two British soldiers named Smythe-Barret, nickname Jingles, and Sgt. Day. They are observing when Destro is taken away to jail.
Lady Jaye goes undercover as a little old lady to gain access to Destro's jail cell. As she is inside, the wall is blown apart and Destro escapes from jail.
A deal is made between them, Flint and Lady Jaye will help Destro get his title and castle back, and the Joes will get the complete plans to the Cobra Terror Drome.
In order to break into the castle, they get an old World War II glider that will help them get through the defenses. Destro, Lade Jaye and Smythe-Barret fly the glider directly into the center of the castle, as Flint and Sgt. Day make a frontal assault by truck. They all fight their way to the plans. The imposter, who has taken the plans, is making his escape. As the real Destro catches him, they fight. Both dressed the same everybody watches to see who wins. Eventually, the real Destro wins, and the imposter is revealed to be Major Bludd.
Destro, now reestablished as the leader of his family's company, holds to the deal he made with Flint and Lady Jaye. He gives them the Cobra Terror Drome plans
On a mission in the Middle East, Dusty and Mainframe have linked up with a local group lead by Professor Gamal. They help him win an ambush against Colonel Sharif's men. In return, they get a motorcycle and a guide. The guide is 13 year old Rashid.
Rashid is very negative towards Mainframe because he is not a soldier like Dusty, but Dusty keeps reminding Rashid that he should not underestimate Mainframe just because he is all about computers. Rashid doesn't believe him.
Their destination is a Cobra Terror Drome hidden in an oil storage tank. They must first cross a desert, where Dusty takes out a patrol that was following them. Upon arriving at the oil field, they gain access to the Terror Drome. Their mission is to gain a real functioning computer from a Cobra Terror Drome. Once inside, Mainframe uplinks through the phone line to Fort Wadsworth, where Hawk, Stalker, Flint and Scarlett receive the information. The mission is complete.
A couple of guards knock out Dusty and hold Mainframe & Rashid at gun point. Mainframe acts weak and when the guards are off balance he takes them out. As they try to escape, they get pinned down by Colonel Sharif's forces. Mainframe reprograms the firebat, from inside the Terror Drome, to make strafing runs that allow them to escape. Rashid has gained respect for Mainframe and computers.
In Denver, Colorado, Cobra Commander has taken his comatose son, Billy, to a Crimson Guard secret research lab. One of the Crimson Guard Fred Series runs the shop, he is Fred VII and his specialty is movement enhancement duplication, robot arms and he has created a new suit of battle armor fit specifically for Cobra Commander. The lab is also filled with hawks that have been specially bred.
Cobra Commander puts on the battle armor suit, which fits him perfectly; it is loaded with sensors, is bullet proof and amplifies his strength. Later, Billy wakes up for the first time in over a year, and can't remember his name or recognize his father.
At Fred VII's garage, Cobra Commander is in his new battle armor. And Billy is about to test his new leg. As he takes the first step he stumbles, then suddenly doing a somersault landing in a martial arts pose. Since he has lost his memory, after being in coma for over a year, he doesn't know how he learned to move like that, but he knows the name of the move.
In Central Utah, Grand Slam, Steeler and Thunder are testing a new artillery unit, protected by Tunnel Rat. Crank Case and Dusty give them the orders to pack up. The convoy, which also includes Hawk, Clutch and Cross Country, head to Colorado. Along the way they pick up Outback, a survivalist expert.
Raptor is introduced to Cobra Commander, who immediately starts calling Raptor names and making fun of his appearance. Raptor is dressed with a long cape covered in feathers and has trained hawks that are able to track and find things. But his day job is as an accountant. In order to prove himself to Cobra Commander, he pulls up information about a Joe who has just had his pay records transferred to a base in Colorado. This Joe is Tunnel Rat. So Raptor, Fred VII and Cobra Commander take off to find him and verify if the now nomad unit of GI Joe can be tracked by their pay records.
Raptor's hawks find the Joes, and Cobra Commander in a Pogo attacks them. A small battle happens with very little damage, but Cobra Commander is reenergized to return to leading Cobra.
Back in Denver, Billy leaves the garage to explore the area, he comes upon a marital arts training center, seeing this brings back the memories of his ninja training that he received from Storm Shadow. The leader of the center is the Blind Master. Billy sneaks into the building but the Blind Master is aware of him. He then introduces Billy to Jinx, who gives him a test. The same test that Storm Shadow had giving to him, this test brings back all of his memories. Billy quickly reacts to the test, and pulls up Jinx's right sleeve. He reveals the Arashikage tattoo on her forearm, which proves her relationship to the Arashikage Clan. Jinx then divulges that they have been watching Fred's garage because they knew that there lives where meant to intertwine. So they have waited.
Hawk has just been kidnapped by Law & Order and Lt. Falcon. They take him to a building that is a complete facade containing a working but old solid fuel missile. At this building, Hawk meets Chuckles and Fast Draw.
Chuckles explains the situation to Hawk. That Lt. Falcon, Fast Draw and Law & Order were assigned to guard this missile. They were also under the assumption that they were part of the GI Joe team, which of course they aren't. Chuckles, had been investigating a high ranking government official with ties to extremists within the Pentagon, when he discovered this operation which is actually a covert op within a covert op. And the missile is targeted for Cobra Island.
Zarana and Buzzer arrive at their hide out in New Jersey. They discover Zanzibar and Monkeywrench stealing gas. After a brief fight, Zanzibar stops the fight by telling Zarana about the missile hidden in a building.
Zarana (in disguise as a casino tourist) busts into the room, just as Chuckles is finishing his story to Hawk.
In Washington DC, the Generals, that Chuckles is investigating, are aware that he is talking to Hawk, so they activate the remote that fires the missile.
As the fight between the Dreadnoks and quasi Joes team members starts, the missile begins its pre-launch procedures. Zarana sends Buzzer to the Cobra Consulate building in New York City to get back up, additionally to warn Cobra Island about the possible missile that is coming there way.
Chuckles fights with Zanzibar, Lt. Falcon fires at Zarana, Order bites Monkeywrench, and Fast Draw tries to destroy the solid fuel missile to stop its launch. The missile fires anyway and is now headed to Cobra Island. All of a sudden an air to air missile intercepts it destroying it. Buzzer shows up with Cobra support and Zarana with the rest of Dreadnoks escape.
After the area is clear, Hawk tells Chuckles, Lt. Falcon, Fast Draw and Law & Order that "as far as he is concerned all of you are now on the GI Joe team for real."
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