I love Darko's synopsis of who Serpentor is, and where he came from!

I'm sure someone at Hasbro was told to "think outside the box", and took some "sleep aids"... LOL

I liked the comic book version better because it kinda fit the "just after tomorrow" sci-fi vibe Joe tried to use throughout its run. The whole Cobra-La secret world story just seemed too much a stretch for me. All you had to do was spray Ortho Weed-Be-Gone and Cobra-La shrivels up.
Besides I liked how Serpentor introduced factionalism into Cobra. Factionalsim was a big part of the real world terrorist movements in the late sixties, seventies and eighties, if they couldn't get their enemies or they won, they quickly started eating their own, so for me it helped make Cobra more "real".
Even now, I divide my Cobra forces by who the troopers should be loyal to. The Baroness gets the Eels and Special Forces Troops. Major Bludd the regular troops, Mindbender the technical troops etc.

Serpentor's origin was Sunbow editor Buzz Dixon's idea, Hasbro intended to introduce Cobra Emperor as "Cobra Commander's boss" and having "been there all along, we just haven't seen him yet" according to Dixon. Dixon told them that didn't make sense and Hasbro told him to come up with some ideas, he pitched two ideas, one that there was another unseen power behind Cobra (Cobra-La) and the other was that Serpentor was created to replace Cobra Commander. Hasbro chose both (Dixon preferred just the latter), so Cobra-La exists because of Serpentor.

Hasbro dropped the Serpentor bombshell after production had already started on Season 2, so any episode Serpentor feels shoe-horned into, he probably was.