G.I. Joe #140 (September 1993) – “Goin’ South” – Larry Hama/Chris Batista/Chip Wallace
This one starts with Megatron taking Cobra Commander and his crew to Canada where the Decepticons’ Ark is hidden. They’re amazed by the Ark’s technology, especially Sidney Biggles-Jones, but Scarlett suggests that once Dr. Mindbender is revived Cobra Comaander won’t need Sidney’s brainpower anymore. Back in Trans-Carpathia, Destro, Baroness, and Zartan paraglide into the castle and manage to take out a squad of Vipers with a little help from Zartan’s chameleon abilities. Meanwhile, Cobra Commander takes
Megatron and the Ark to Milleville, the town full of brainwashed citizens conditioned to obey his every command. While they’re unloading, the brainwashing wears off one citizen, who causes a disturbance that ends up with Dr. Mindbender’s body being freed from its stasis tank and zapped with high voltage. That revives him and naturally he’s not too happy with Cobra Commander, who’s the one who killed him in the first place. But when he sees Megatron, he reconsiders his options (and I find it interesting that Mindbender recognizes Megatron as a Decepticon). Outside of town, a force of Joes has 
gathered after getting info about Cobra’s recent movements. Hawk sends Tunnel Rat, Roadblock, Rock n’Roll, and Airtight in through the sewers, while the Joe Ninja Force hitches a ride on an Arbco truck. The ninjas head to the hospital to find Scarlett and spot Mindbender catching up on what he missed while he was dead. (He’s very disappointed that there’s a Democrat in the White House, that Cheers got cancelled, and that Michael Jackson no longer looks like Michael Jackson.) The ninjas find Sidney in Scarlett’s room, letting Scarlett know that Sidney’s aware of her being a double agent. Snake Eyes overhears and prepares to take Sidney out, but I’m thinking Sidney is
also undercover, since there was mention of a spy inside Cobra tipping the Joes to their movements. When the Joes spot Megatron, they radio Hawk who passes the message on to the Autobots on Cybertron through a dimensional warp. Yeah, things are about to get more even weird. I’ve said before that I don’t like the Transformers stuff mixing with the (somewhat) more realistic Joes, but I guess we’re stuck with it. I am interested to see what plan Mindbender is hatching, as he seems to be more of a mastermind than the goofball he was before.
G.I. Joe #141 (October 1993) – “Sucker Punch” – Larry Hama/Steven Lieber, William Rosado/Chip Wallace, Scott Moulter
This one continues from the above issue, with the Joes in the sewers running into some Eels and taking them out, but not before they get a signal out. Cobra Commander orders teams into the sewers and asks Megatron for help, but he says the deal was a simple trade: Decepticon tech for Sidney Biggles-Jones. Speaking of the doctor, she’s still in Scarlett’s hospital room accusing her of being undercover for the Joes. The Joe ninjas observing outside are jumped by Night Creepers, who they take out quickly. They get a call to help the team in the sewers and take off, leaving Snake Eyes to deal with the Night Creeper leader and check on Scarlett. It looks
like my guess about Sidney spying on Cobra was right, but she doesn’t know Mindbender is listening through the wall and has just been backed up by Slice and Dice. Megatron shows up to claim Sidney before leaving (although he apparently only needs her brain and central nervous system intact) and Mindbender sends Slice and Dice to capture Scarlett. She hides under the bed and jumps them, taking them both out before going to rescue Sidney. Meanwhile, Snake Eyes’s duel with the Night Creeper leader has proved to be a stalemate, until Snake Eyes confuses his opponent with some more esoteric moves, taking him down. The Joes in the sewers get out but are told by Hawk that their whole team has to leave since the government already has n agent 
inside Cobra (who I assume is Sidney) and they don’t want that operation compromised. Hawk does let Storm Shadow and Spirit go back to get Snake Eyes out. Speaking of which, Snake Eyes gets jumped when he arrives at Scarlett’s hospital room and is quickly surrounded by Cobras. Outside, Scarlett confronts Megatron (with a sword!) and demands he let Sidney go. This issue was pretty good, although the ninjas and Transformers seem to be taking over. We never actually hear Sidney say she’s a spy, so I’m wondering if the informer inside Cobra will turn out to be someone else and Sidney’s story will have some kind of twist to it.