G.I. Joe #49 (July 1986) – “Serpentor” – Larry Hama/Rod Whigham/Andy Mushynsky
This one starts with Destro and Dr. Mindbender stealing a mummy from a museum in the Middle East and taking it back to Springfield. The Frankenstein parallels continue, with Mindbender planning to extract the DNA from the stolen remains of history’s greatest warriors, mix it together and put it into an artificial body he’s grown, then fill that new creation with historical knowledge to create the ultimate conqueror. (The idea was Mindbender’s, but Cobra Commander is behind him all the way.) Mindbender also plans to add some of Storm Shadow’s DNA to his creation, since Storm Shadow was only killed recently by Baroness. Elsewhere in
Springfield, the Dreadnoks have noticed Zartan’s weird behaviour but haven’t thought much of it until Scrap Iron shows up to tell them someone has called the Joes and revealed the location of Springfield. They realize “Zartan” is actually Ripcord and try to blast him, but he takes off, jacking a car with a kid in it. In the Pit, Hawk mobilizes the entire Joe team to attack Springfield, including some newcomers. In Springfield, the little girl Ripcord accidentally kidnapped pleads for him not to hurt her, but she turns out to be a Cobra through and through as she pulls a gun on him and forces him to stop the 
car. In the lab, Dr. Mindbender uses the brainwave scanner to impart his knowledge of current events (and his allegiance to Cobra) to the new person growing in the vat, who he christens Serpentor. The Dreadnoks bring in Ripcord (who they’ve been pounding on) to use the brainwave scanner on him. The machine confirms that he’s revealed Springfield’s location to the Joes, so Destro prepares to evacuate the whole town. Serpentor emerges from his vat and immediately predicts exactly what the Joes will do. When he’s proven right, Destro gives the evacuation order and Serpentor offers to lead a holding action to delay the Joes long enough for everyone to get away. Destro is skeptical of Serpentor’s loyalties, but agrees
to the plan, leaving Scrap Iron, Firefly, and Mindbender behind to keep an eye on their new ally. (And Firefly has orders to kill Serpentor if he shows signs of disloyalty to Cobra.) As the Joes prepare to assault Cobra headquarters, Serpentor rallies his troops, promising them victory instead of certain death. This issue is important in Joe canon, even though it’s mostly just set-up for next issue. Not only do we get the first appearance of Serpentor, we also see some new Joes (Leatherneck, Slipstream, Lift-Ticket) and 
the new Cobra communications specialists, the Tele-Vipers. A lot of fans think Serpentor is too cartoony (and they’re right), but I’m sure Larry Hama had no choice in whether or not to introduce him and just made the best of it. I think he does a pretty good job, using Serpentor’s presence to create a schism in Cobra with Serpentor and Cobra Commander jockeying for power and everyone trying to choose sides. That will ramp up the tension for quite a while, keeping the series interesting.
G.I. Joe #50 (August 1986) – “The Battle of Springfield” – Larry Hama/Rod Whigham/Andy Mushynsky
This one starts some time after the end of last issue, with the battle already raging in the streets of Springfield. Stalker’s team has clashed with Serpentor’s troops and Stalker has found that Serpentor can anticipate his strategy quite well, not to mention acting as something of a talisman for the Cobra soldiers. Scarlett and Recondo are wounded and the team has to retreat, as Serpentor is pushing towards the airport. Hawk tells Stalker to hold out as long as possible so they can get reinforcements to the airport, just as Serpentor rallies his men again and
pushes forward. Meanwhile, the real evacuation is taking place across town, with Springfield citizens assembling at the local high school. As the other Joes regroup at the airport, the Dreadnoks discuss Zartan’s whereabouts (now that they know Ripcord has been impersonating him) and Buzzer tells them he knows where Joe headquarters is. When Ripper tries to steal the swords from Storm Shadow’s corpse, the supposedly-dead ninja rises up to stop him. As the covert evacuation continues, Baroness questions why Destro is helping Cobra Commander and Destro says it’s a matter of honour, suggesting that honour might be more important than love to him. 
At the museum, Storm Shadow seems like he’s not really alive or dead, but is filled with memories from the DNA that created Serpentor. When the Joes assault the museum, Storm Shadow elects to flee and the Dreadnoks go with him. The Joes find Ripcord, who warns them the museum is wired to blow up. And that’s not the only place that’s wired; Zap finds a tunnel network under the airport and realizes Cobra could’ve moved all their air transport across town. His theory is confirmed when Cobra blows the entire tunnel system in preparation for their real evacuation. Stalker’s team arrives at the airport with Serpentor’s men right behind them, but the Cobra vehicles disappear and the Joes almost blast some of their own men. The Cobra show up again with the engines even louder than before, but it turns out to be another
fake-out to cover the sound of the transport helicopters landing to pick up Springfield’s citizens. Serpentor’s plan worked perfectly and he thanks Baroness for coming back to save him (even though that was Destro’s idea and Baroness wanted to abandon Serpentor). The Joes realize they’ve just obliterated a small town with no real proof it was a Cobra stronghold and on Cobra Island, Cobra Commander suddenly gets paranoid, wondering if Serpentor means to take his place. Meanwhile, the Dreadnoks and Storm Shadow arrive at Zartan’s gas station hideout in New Jersey, but find it already occupied … by Zartan’s sister, Zarana. This is a great conclusion to the battle for Springfield, with the Joes coming out looking bad and Serpentor showing his military genius by out-thinking them at every turn. 
We also get our first look at Zarana, who I always thought was kinda hot, despite (or maybe because of) her weird sense of style. Originally, issue #50 had a back-up featuring the first Special Missions story, with select Joes going on various missions (special ones) all over the world. I will be reviewing the Special Missions series, but this first story is pretty basic: some terrorists hijack a plane and a few Joes (Flint, Beach Head, and Lady Jaye disguised as a flight attendant) get aboard covertly to take them down. The thing I liked about Special Missions was that the Joes usually fought enemies other than Cobra, but after a while it got a bit repetitive too, since most terrorists are rather similar even though they claim to have differing ideologies.