I like this realistic aproach. Where does Raptor fit into your Joverse? If you use him at all?

In My JoeVerse, Serpentor is much Like GITom said. Third Clone. V1 was created by Dr. Mindbender as a replacement for Cobra Commander. Cobra Commander funded the Project thinking he was getting the Ultimate battlefield commander. When it was realized that Serpentor was meant to replace him, the Cobra Civil war broke out. Serpentor was killed by Zartan. MindBender hedged his bets by cloning Serpentor (and himself) and hiding the technology, clones and his notes in Various Places. Cobra Commander is FURIOUS and wants the destroy the Serpentor Project.

MindBender keeps one step ahead by downloading his consciousness every so often into a computer program that can reload it into a Clone much like the "Synch Cord" in the Schwarzenegger movie "The 6th Day".

Serpentor 2 was one of these clones as was Mindbender. The events happened pretty much as the devils Due comic portrayed them. Another War between the Coil and Cobra. Although Cobra Commander destroyed the coil, some hardcore loyalists escaped and began rebuilding. Along the way, they infiltarted Cobra (And MARS) and have sabotaged Cobra Commanders efforts and put strain on his and Destro's relationship.(Because of this, Cobra is depleted and Cobra Commander started the Venom 2 Project which failed with the exception of Sgt Riddick) Mindbender has escaped Cobra (See Enemy of my Enemy # 2) and is getting ready to create Serpentor #3.

I haven't gotten to that part yet, but #3, being the best version of Serpentor yet, will realize that he cannot take over cobra, and he an the Commander will be forever locked in a duel, depleting both Cobra and The Coil. He also knows any other Army large enough to take over the world will not have him because he's FAR too dangerous. So he will strike up a bargain. He will be Cobra Commanders new General, he will lead the Armies of Cobra for Cobra Commander, but cobra Commander has to give him TOTAL control of strategic and Tactical Decisions. Cobra Commander says "Take country X" but Serpentor decides HOW to take Country X. Like Swindle said, if CC and Serpentor can unite, they can take over the world. But on the way, they will need to cut deals and bolster their forces with groups like Destro and his Iron Grenadiers, Headman and his Headhunters, The Skull Troopers, the Dreadnoks and maybe even a newly formed Oktober Guard! The new Serpentor MArk 3 is not only the ultimate battlefield commander, but a skilled Politician and master manipulator.

The fun is just begining in MY JoeVerse!