This issue contains two stories - Operation: Lady Doomsday and Hot Potato.
Operation: Lady Doomsday - The Joes are sent in to rescue Dr. Adele Burkhart from the clutches of COBRA before her secrets are revealed.
Hot Potato - Scarlett, Snake-Eyes and Rock 'N Roll are tasked with getting a tape containing sensitive information out of Colonel Sharif's tightly controlled emirate.
Operation: Lady Doomsaday
The story starts off with on a train in the middle of New York City and Washington DC, where a woman, named Dr. Adele Burkhart, is holding a press conference in one of the rooms. Dr. Burkhart is in charge of a nuclear weapons program. In the next shot, a group of terrorists, known as COBRA skydive and attack the train. A couple of reporters reveal themselves as COBRA operatives and had used the cameras as guns. One of the operatives, named Baroness take Dr. Burkhart into a helicopter.
In the Pentagon, General Flagg and General Austin discuss on how to rescue Dr. Burkhart before she reveals her secrets to COBRA. Flagg considers a counter terrorist group named the G.I. Joe. Austin pulls up the records of all the members and heads on down to their headquarters. Austin begins briefing the members on the operation.
At the COBRA Island, the COBRA Commander begins to taunt Dr. Burkhart. A COBRA operative notices and alerts the Commander of an incoming force. COBRA immediately deploys a force to counter the incoming squad of Joes. The G.I. Joe also notices the COBRA squad on the beach and they send Stalker in. Stalker nearly wipes out the COBRA forces on the beach. The rest of the Joes reach the beach and begin mapping their targets.
Meanwhile, at COBRA HQ, COBRA Commander and Baroness begin arguing on how they should counter the G.I. Joe. Baroness argues that they should execute Dr. Burkhart and send in teams to eliminate them, while COBRA Commander insists that the should let them come and try and take Dr. Burkhart.
Behind the COBRA Radar site, Breaker and Flash tap into their radar sites. Back at the HQ, Scarlett and Snake Eyes discover Dr. Burkhart tied to a chair. Scarlett begins on contemplating on shooting Dr. Burkhart, but back outs of it. Later on at the airfield, Grunt, Stalker, and Short-Eyes prepare for their assault at the airfield. Meanwhile at the Pentagon, Flagg and Austin begin the movement of a second force, armed with armored vehicles that will be deployed to combat the COBRA forces. Back at the airfield, Short-Eyes fires a mortar onto the airstrip, destroying a couple of planes. Grunt and Stalker begin laying fire onto the remaining planes, destroying the airstrip in the process. Grunt comments on how easy it was. A COBRA operative radios in that the intruders had destroyed the dummy planes.
Scarlett and Snake Eyes begin taking out some of the guards at the HQ, while Breaker and Flash run into Grunt, Stalker and Short-Eyes. Baroness begins to argue that they should execute Dr. Burkhart, as the Joes have already destroyed the airstrip. COBRA Commander reassures her that is plan is going out fine. A COBRA operative informs the Commander that another force of Joes has landed on the beach.
The second force of Joes begin destroying many of COBRA forces. Meanwhile, Snake Eyes and Scarlett take out the main generator. One of the COBRA members notices and orders Baroness to take Dr. Burkhart to take her to the airfield. At the fishing village, Flash, Breaker, Stalker, Grunt and Short-Eyes discover the dead bodies of the villagers. Later on, the second force of Joes destroy three tanks and a large amount of soldiers. Stalker ambushes a COBRA squad that was escorting Dr. Burkhart. He takes her from the wreckage and discovers that it was Baroness in disguise.
Back in the COBRA HQ, COBRA Commander assures Dr. Burkhart that his plan is going accordingly. Nearby, a COBRA soldier destroys the Joes tank, forcing the Joes to abandon it. Back at HQ, Scarlett and Snake Eyes fight their way through the HQ and discover Dr. Burkhart being held by COBRA Commander. COBRA Commander holds her hostage, forcing Scarlett and Snake Eyes to drop their weapons. The other Joes have a firefight with COBRA forces and begin to wonder where the Scarlett and Snake Eyes are.
Meanwhile, COBRA Commander tells the two that they will wait five minutes for the steel door to open, until Dr. Burkhart reveals that it's a trap. He attempts to shoot Snake Eyes, but Dr. Burkhart prevents it from happening. Scarlett reveals some ninja stars underneath her sleave and throws it at the COBRA Commander, injuring him in the process. The rest of the Joes blast the door open and find Dr. Burkhart wounded. She thanks them for their efforts and they take her to a helicopter. The Joes later find out that COBRA Commander had escaped through the a hidden passage way. They realize it's too late to chase them and go into the chopper. Right after they take off, the HQ explodes, destroying the Joes vehicles in the process. The chopper flies away, while Baroness and COBRA Commander escape through another plane and decide to rest until later on.
In a Middle Eastern village, Clutch, Stalker and General Hawk discuss plans on the capture of Colonel Sharif, a leader of a terrorist group known as Guardians of Paradise. The mission was to extract a tape that had information on Colonel Sharif. Meanwhile, in the desert, Snake Eyes, Rock N Roll and Scarlett have recently finished a firefight and were informed that another force of soldiers were coming their way. Scarlett was shot in the leg and is forced to stay behind while Snake Eyes and Rock N Roll to deliver the tape. The two begin running until Rock N Roll had lost Snake Eyes.
Scarlett is able to hold off the soldiers until two of them come from behind. They tried to throw a grenade until someone shoots them from behind. Snake Eye appears and reinforces Scarlett. Back at the village, someone throws an object at Clutch, Stalker and Hawk, making them to think it was grenade. They realize it was the tape they were looking for. They notice Rock N Roll driving back to the desert in his motorcycle. They realize that Scarlett and Snake Eyes were alive and need help.
Rock N Roll races to where Scarlett and Snake Eyes while another force of Sharif's forces rally. Sharif's soldiers begin charging at the two and hold them off through machine gun fire. They find Rock N Roll, where he eliminates a few targets. Scarlett and Snake Eyes hop into the motorcycle and drive away. Colonel Sharif orders an airstrike against the the three, where a fight jet is deployed. Just then, Hawk destroys the aircraft with anti aircraft artillery. Scarlett asks where the tape was, and he reveals it's with Stalker. On a plane, Stalker decides to order a hot potato.