It might be in 4e, but I believe it was described in one source as a creature that failed in its attempt to ascend to godhood. That seems pretty easy to explain, it has the added bonus that ascending to godhood is supposed to difficult, treacherous, and almost, if not completely, impossible to discovery how to do (so you don't and shouldn't go into details).
I figured you'd be hip to that.
Mainly posting it for general consumption because I've seen lots of DMs who get hung up on 'staying true' to fluff in some way. I just want to reiterate that you don't need to. When you sit behind the DM screen it becomes your story, and for many that's the appeal of DMing in the first place.
I think I've found something that will work for me...
The atropal is Kyuss, The Worm That Walks, who is supposed to herald destruction of the world by undead.
While reading some of the Adventurer's League material for ToA, I stumbled on DDAL07-06 Fester and Burn where spawns of Kyuss appear without any explanation. That seemed weird, so I checked Kyuss' wiki entry (linked above) and found non-canonical information placing him in Chult – this was from Paizo's Age of Worms adventure path apparently – where he's described as a fallen prophet of Mezro.
Having never used Kyuss, I read more, learning that he sought godhood but his ritual was stopped...which seems to match the conception of an atropal you gave @dave2008.
[SBLOCK=Non-canonical background on Kyuss]Non-Canonical Background
According to legend Kyuss was an extremely powerful tabaxi (AD&D Chultan tribe, not cat-people, yeah it's confusing) and a charismatic prophet in Mezro who led his cult out of that city in -653 DR after persecution from the mainstream followers of Ubtao. He wanted to become an obscure deity of the Chultan Peninsula.
Kyuss and his followers founded the religious city of Kuluth-Mar in the Chultengar. His cultists discovered ancient metal plates that foretold the future and confirmed every prophecy that Kyuss had ever made. Kyuss was personally visited by his god, Jergal, who gave him a gift of a single green worm and tutored the man in the ways of necromancy
He began experimenting on the undead, creating such horrors as the Kyuss worm, the spawn of Kyuss and the avolakia. At this time, he gained the services of the red dragon, Dragotha, who he transformed into a dracolich to serve as his general of his undead host. He created a cult around the dogma of life being only temporary, the afterlife a lie and undeath being the one true path to immortality.
While his cultists grew ever more devoted by the apparent truth of his visions, Kyuss tried to fulfill the greatest of his prophecies. He sacrificed powerful magic items and built a massive citadel, the Spire of Long Shadows. At the top of the Spire, he created a monolith through which he channeled the terror, adulation and souls of his entire cult and achieved apotheosis.
However, an alliance of couatls, eladrin wild dwarves and druids trapped him in the monolith, which prevented him from ascending to true godhood and relegated him to a historical footnote.
Two millennia later, a coalition of banites, Bhaalites and Myrkulites known as the Ebon Triad who sought to resurrect their dead gods, initiated a plan to free Kyuss and use his divine spark to achieve their objectives.. In reality, the Triad was created by Kyuss's high priest, the silver dragon vampire Lashonna, who is utterly devoted to him to the point of love, and an avolakia who in its disguised form serves as the Triad's leader.[/SBLOCK]
Dungeon 130's "The Spire of Long Shadows" has a whole ruined city (Kuluth-Mar) and a ziggurat in the jungle where Kyuss tried to ascend and failed, making it a decent way to get information to the players about what the atropal is. The supplementary material to Dungeon 130 places this ziggurat in the Chultengar – which fortuitously just happens to be a large swath of jungle in Eastern Chult which previously had no description or reason to explore in ToA.
Kyuss seems to be depicted as a giant wraith made of worms, at least in later incarnations...thematically that's something I could tie into the yuan-ti in Omu or Hisari, dropping hints of yuan-ti heretics revering Kyuss. This would also be a more palatable depiction for my players than "aborted fetus monster."
Even the pronunciation of Kyuss' name ("Kai-ess") seems kind of Chultan.
Acererak is using Kyuss' deep connection to undead – especially undead of Chult – to gain control over all undead everywhere. Essentially, Acererak aims to make all undead his mouthpiece/phylactery. He does this so he never need fear death by adventurer; shaking off the confines of lichdom to become something more powerful, to become Undeath itself. This is pretty much his goal from Return to Tomb of Horrors that you mentioned @Mouseferatu, just a bit more spelled out. This opens up some cool interaction "with Acererak" via mouthpiece zombies before the PCs possibly encounter him in the Tomb of Nine Gods.
Using Kyuss is a really inspired choice. Great idea! However, as is often the case in the Forgotten Realms, a plan like that is pretty much doomed to fail because of some mind boggling powerful NPCs who are entirely capable of putting a stop to such a thing. Granted, there is always the fall back of "But they were busy doing other things at the time", but this particular goal is... really an eye catcher. It's going to set off some major red alarms, unless the party is already part of a counter-plot against Acererak.Acererak is using Kyuss' deep connection to undead – especially undead of Chult – to gain control over all undead everywhere. Essentially, Acererak aims to make all undead his mouthpiece/phylactery. He does this so he never need fear death by adventurer; shaking off the confines of lichdom to become something more powerful, to become Undeath itself. This is pretty much his goal from Return to Tomb of Horrors that you mentioned [MENTION=1288]Mouseferatu[/MENTION], just a bit more spelled out. This opens up some cool interaction "with Acererak" via mouthpiece zombies before the PCs possibly encounter him in the Tomb of Nine Gods.