G.I. Joe #108 (January 1991) – “Apparent Conclusions” – Larry Hama/M.D. Bright/Randy Emberlin
This one starts in Trucial Abysmia, the (fictional) Middle Eastern desert country the Joes have been to a few times before. A contingent of Joes (including Duke, Lt. Falcon, Doc, Quick Kick, Heavy Metal, Cross Country, Crankcase, Crazy Legs, Thunder, and Breaker) are blowing up a Cobra Terror Drome before heading back across the border, but they notice a lone Cobra vehicle making a run for it. They have to stop the Cobras before they can get outside jamming range and call for back-up, so they chase the vehicle into the desert but soon find themselves surrounded by Cobras in an ambush. In New York, Snake Eyes has returned from Borovia (with the orphan
Marina in tow) and goes to the hospital to see Scarlett. General Crowther is still an asshole but Stalker fills Snake Eyes in on everything that’s happened, including Scarlett and Storm Shadow supposedly being run down by a subway train. Snake Eyes takes Stalker to a secret hideout under Columbia University, where they find Scarlett and a badly wounded Storm Shadow (from Scarlett stabbing him when she thought he’d sent Snake Eyes to his death). Snake Eyes uses the Arashikage mindset to stabilize Storm Shadow so they can get him to a hospital, now that they’ve been cleared of any wrongdoing in the 
Borovian boondoggle. In Trucial Abysmia, the Joes soon find the tables turned, with them surrounded and unable to call for help because of Cobra’s jamming. They lose the Warthog and HAVOC, forcing them to crowd onto the Mauler and AWE Striker, but Cobra has them boxed in completely so they have no choice but to surrender. In New York, Snake Eyes figures out that Cobra is using the burnt-out remains of their consulate as a hideout and goes there (with Stalker) to confront Cobra Commander. They give the Commander an ultimatum: leave New York forever or die right now. In Washington, Hawk tells Crowther to back off his vendetta against Snake Eyes and Storm Shadow, since Magda (the new leader of Borovia) knows al about his double-dealing ways and
could go public about it. Later, Snake Eyes, Scarlett, Stalker, and Storm Shadow take Marina to Wade Collins’s place to be adopted into his family. This was a pretty good story, with an end to the Borovian stuff (although Crowther might not be inclined to give up so easily) and to Cobra’s New York adventures (at least I assume that’s the option Cobra Commander chose). But we’ve also got a bunch of Joes taken prisoner in Trucial Abysmia and it looks like Tomax and Xamot aren’t likely to release them anytime soon.
G.I. Joe #109 (February 1991) – “Death in the Desert” – Larry Hama/John Statema/Tim Dzon
This one starts where the above issue left off, in Trucial Abysmia with Tomax and Xamot kicking the shit out of Duke. He pretends to be more hurt than he is, but the Cobras herd all the Joes into a ravine and call Cobra Commander for orders. He’s getting ready to evacuate New York after Snake Eyes’s threat last issue and tells them to get rid of the Joes (although he later tells his men in New York he ordered the Joes released … plausible deniability, I guess). Tomax and Xamot are worried about executing the Joes—not necessarily out of
morality but just because it could cause an international incident and get them (and Cobra) in a lot of shit. The Vipers feel the same way, but a Saw Viper finally agrees to do the job as long as he gets a bonus. Tomax and Xamot leave he Saw Viper and a couple of regular Vipers to take care of the Joes, while they lead the rest of Cobra’s forces to their next objective. Doc gets shot first trying to see what’s going on, then the Saw Viper sprays bullets into the ravine, killing Crankcase, Heavy Metal, and Thunder. Lt. Falcon uses a knife that Cross Country took from a Viper that was pounding him to kill the Saw Viper and 
Quick Kick gets his gun and wastes the other two Vipers. They use the Cobra vehicle to call the Pit for help before Cobra gets wise and jams them. Tomax sends a few Cobras back to wipe the Joes out and in the Pit, Hawk orders the space shuttle Defiant to get ready for launch. The Joes head for the border, but don’t realize the Saw Viper is still alive (saved by his body armour) and joins the other Cobras hunting them. The Defiant reaches space, comes back into the atmosphere over the Middle East and deploys a mobile battle bunker with Rock n’Roll, Clutch, and Wildcard in it to reinforce the Joes in trouble. But it looks like they’re too late as the Cobras attack the Joes and overwhelm them, losing a few Cobra vehicles but finally blasting the Joes. Only Duke, Lt.
Falcon, and Cross country survive the blast and they’re quickly surrounded by Cobras. The mobile battle bunker deploys parachutes, but the lines break and they plummet toward the ground at deadly speed. So yeah, this is the infamous issue with five Joes getting killed. I think this was a response by Larry Hama to all the readers who complained that the comic was unrealistic because no Joes ever died in the numerous battles. Well, there’s some dead ones now, including old favourite Doc. We’ll have to wait and see if the body count goes up next issue.