G.I. Joe Special Missions #1 (October 1986) – “That Sinking Feeling” – Larry Hama/Herb Trimpe
This one starts with a team of Joes (Cutter, Shipwreck, Torpedo, Wetsuit, and Deep Six) aboard a Swedish trawler (the Christina) in the Baltic Sea. They’re obviously not there for the sights and we see the Russians have sent the Oktober Guard to check them out, with Colonel Brekhov and Daina flying over them in a HIND chopper. Brekhov assumes the Joes are there on a secret rescue/retrieval mission, before he can decide what to do about it, Baroness leads a couple of Cobra
FANGs in an attack on the Russians. Apparently Cobra is interested in whatever’s going on too. After a dogfight between the choppers, both sides are forced to head back to their bases because of battle damage, leaving the Joes to go ahead with their mission. That mission involves Deep Six heading underwater in the SHARC with an A/V cable attached for some reason. Brekhov and Daina land on the ship Udaloy, whose captain (Bulgakov) seems like a fervent Communist. We find out that an American submarine was lost in the vicinity, which makes Brekhov think they must’ve been equipped with some pretty fancy tech to even make it that far into the Baltic. 
Naturally, the Russians want that technology for themselves, as do Cobra. The Udaloy confronts the Christina and while Bulgakov and Cutter parley, Daina and Horror Show splice into the Joes’ commo cable to see what they’ve found. The intercepted feed confirms there’s a disabled sub on the sea bottom. Baroness shows up in a hydrofoil with Firefly and some Eels and they soon learn about the sub and attack the Udaloy, trying to knock it out of the fight. Daina boards the hydrofoil and blows up the controls before getting kicked off by Baroness. Horror Show locates the SHARC but is puzzled to
find a VCR inside and is so distracted he doesn’t notice Deep Six sneaking up on him. Since the hydrofoil controls are out, they end up ramming the Udaloy and the Cobras engage in a firefight with the Oktober Guard. While that’s going on, Torpedo and Wetsuit covertly board the Udaloy with a special harness for Captain Bulgakov. Destro shows up in a Cobra submarine to put an end to the fight and explain the Joes true mission … picking up Bulgakov, who’s defecting to the West. Apparently his loyalty to the Party was shattered when his wife died, since her Jewish heritage kept him from advancing in the Party ranks. Bulgakov is successfully extracted and the 
Joes dump Horror Show into the sea before leaving. The Oktober Guard reluctantly return Baroness and Firefly, but Brekhov’s pissed off about being taken in the the Joes’ ruse. This is a pretty good start to the new series, which will feature the Joes fighting various threats besides Cobra. Of course Cobra are involved in this story, but they spend most of their time fighting the Oktober Guard instead of the Joes. In fact, as Wild Bill points out, the Joes managed to pull off their mission without firing a shot. It’s nice to see the Oktober Guard again, who quickly became fan favourites, and who will be popping up in future issues.
G.I. Joe #53 (November 1986) – “Pit-Fall” – Larry Hama/Rod Whigham/Andy Mushynsky
This one starts with three top brass types (General Ryan, General Hollingsworth, and Admiral Dyson) showing up to inspect the Pit, which has been shut down after the Joes big fight in Springfield a few issues ago. The brass are there to decide whether to shut down the Joe team permanently or not, with Hawk trying to convince them the Joes are essential to the security of the country. Hollingsworth seems to be on Hawk’s side, Ryan wants to shut them down, and Dyson is on the fence. The Joes are on inactive status, confined to the Chaplain’s Assistants’ tea room, where their rough ways disrupt the normal order of things. Cobra
picks this time to attack the Pit, showing up in force with Cobra Commander and Serpentor both planning how to achieve victory (and take the credit for it). Outside, Flint is putting the moves on Lady Jaye (who claims she isn’t interested) when a contingent of eels pops out of the water. Thanks to a ruse by the Zartan family, the Cobras get into the motor pool and unleash some BATs (Battle Android Troopers) into the Pit. Hawk and the generals see what’s happening on the security cameras and drop the BATs into the lower levels, but the broken parts still keep shooting. Hawk and the generals arm themselves with some heavy artillery and start fighting back, but are forced to retreat to the lower levels. Outside, Flint jumps the Eels so Lady Jaye will have time to warn 
their teammates about Cobra. She finds that Spirit, Quick Kick, and Cross Country already know about the invasion but aren’t sure what to do since all their weapons are locked up. Cobra Commander decides to lead some troopers down into the Pit to root out the resistance there, and to show up Serpentor. Destro volunteers to join him and they head underground. Flint gets the shit kicked out of him, but does take down the lone Eel who was left behind to finish him off. Below the Pit, Cobra Commander sends a BAT strapped with explosives to blow up Hawk and the generals, not caring if some Cobra troopers are caught in the blast. Dyson tackles the BAT, holding it back long enough for the others to escape before blowing the explosive charge. Cobra Commander is ecstatic thinking he’s killed Hawk, but he soon realizes his
error and chases the generals even lower. Hawk and the other two retreat to the service level where there’s a secret escape tunnel. General Ryan sees Cobra Commander and Destro and figures they can collapse the Pit right on top of Cobra’s high command by blasting the main support pillars. Up top, the Joes break into the armory and assault the upper levels of the Pit, pinning Serpentor and company inside the motor pool. Down below, Ryan is pinned beneath some machinery and orders the others into the escape tunnel while he blows the Pit support beams, bringing the whole headquarters down on himself, Destro, and Cobra Commander. As the Pit collapses, Serpentor and 
the Zartans use the distraction to escape, ramming their way out in a fuel truck. Hollingsworth takes the Joes off suspension and tells Hawk they’ll be a nomadic unit from now on so this sort of thing doesn’t happen again. This is a pretty good issue, with the Joes forced to assault their own headquarters and Cobra coming close to winning. It was cool to see Hawk and the armchair generals kicking some ass, showing that they haven’t lost their combat skills. Of course, Destro and Cobra Commander aren’t dead yet, we’ll be seeing plenty of them in upcoming issues. And we’ll be seeing more of the romance between Flint and Lady Jaye, the first sparks of which were kindled here.