I like all of these ideas and I am going to steal them. I think the idea of gith coming from elves. Maybe they hid in the Black Spine mountains during the cleansing wars and drank from an underground stream contaminated by the Pristine Tower.
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I go with the idea that the Githyanki were extraplanar travelers during the age when the planes & gods were accessible to Athas, Because the world’s creatures were naturally psionic, they probably had a significant stronghold populated by enough Gith to propagate the species that would justify their continued existence.
Then during the cataclysm (could be cleansing wars, or something else in your game) that changed the metaphysical alignment of Athas and closed it off they were one of the early victims of the event and something (an Enemy, could be the Githzerai or something else) managed to neutralize them to the extent that it turned them into less refined forms of themselves and were no longer viewed as a threat.
perhaps, every 10,000 of so births, an exceptional Gith is born with the cunning of his ancestors, who resembles the Githyanki of old. If these special births survive the rigors of Athas to adulthood, they are drawn by a dull, yet constant psychic call to travel to a faraway land…none have ever returned.
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I go with the account in Black Spine - degenerate descendants of Githyanki migrants. Black Spine states the githyanki created Yathazor ‘millennia ago’ which means you can fit them in as far back as the Rebirth or as recently as the end of the Cleansing Wars or anywhere in the 12,000 years between those 2 events.
I like the idea that Athas’ planar borders, despite being more or less blokaded from the rest of the multiverse now, at some point were more porous. I also like the idea that not everything on the planet is the result of loony halflings, insane pyreen or evolved/devolved bugs. 
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I subscribe to there was an illithid presence on Athas which is why the githiyanki went to the lengths of creating a city on the prime material.
Also believe it was much easier reaching Athas in its infancy. A planar accident occurred in the Blue Age which has made it increasingly harder to breech Athas’ boarder Ethereal and Astral.
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The accident in question could have been a living vortice reaching to deeply into the Negative Energy Plane causing it to spill into both Athas’s boarder Etheral and Astral creating the Gray and possibly the Black.
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I looked up the 2E entry for gith. Like the regular githyanki, they are egg layers.
Habitat/Society: The gith live in tribal organizations. The individual with the most powerful psionics generally acts as the leader. All other social positions are distributed at his pleasure.
For every twenty-five gith, there will be a 5 HD leader, for every fifty, a 6 HD leader, and for every tribe of 100 or more a 7 HD leader. In addition to having hit points and THAC0 numbers appropriate to their HD, these leaders will have psionic powers approximately equal to a psionicist of an equivalent level.
Some of these leaders are priests. While little is known of the gith religion, shamans up to the 4th level are known to accompany and sometimes lead gith tribes. There have also been reports of gith wizards (defilers) ranked at the 6th level. Even if true, 6th level would be unusual for gith, but wizards of up to 4th level have been reported by reliable witnesses.
Not much is known about the reproductive cycle of the gith. It is known that they are egg layers; females lay approximately 1d6 eggs in a clutch. It is rumored that the gith operate hatcheries containing hundreds (some say thousands) of nests.
I wonder if the gith are able to leave their eggs unquickened in a preserved state, to be quickened whenever the circumstances allow. That could account for the gith hordes that emerge from the wastes from time to time.
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I also go with the notion that Athas had illithids on it along with the idea that planar travel was easier prior to the cleansing wars. Maybe not as easy as on some other worlds, but easy enough that illithids and githyanki migrated to Athas. In my campaign illithids are still around, but all the elder brains are dead. Mind flayer society eventually degenerated and neothelids have replaced illithids almost entirely.
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I have illithids in my Sundered Regions part of Athas. For my campaign the illithids were at war with the rhulisti in the early Blue Age over “stealing” mindflayer graft technology to unlock the basics of life-shaping.
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In addition to being a great adventure, that was some great surprises and impressive bit of world building.
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It is a well written segment. However, I think it was more about being as complete as possible for a supplement about elves. AKA it was written for something other than Dark Sun.
The real issue for me is this. It makes no difference as written. How is changing their origin different? In this context, it does not. In essense, it’s academic
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Just hope your realm doesn’t get invaded by giant space hamsters.
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Love this idea. @Killer_DM pointed us to the Dark Sun Ecology netbook which theorized estivation as a primary driver behind the number and diversity of (hazardous) animal life.
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I really like the idea of gith hordes rising after particularly wet years. Maybe humidity or damp eggs break down a bit allowing more of them to take to fertilization?
“When the desert rarely flowers, mark the day. For it won’t be long until the gith rise again.”
This could cause there to be an odd rain worship with the gith… and maybe even the rare rain cleric to come out of their numbers.
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I like that idea Robert. I’ve now got an image of a crazy old Gith rain cleric doing a demented rain dance as part of his control weather spell casting 
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grabs an idea or two off the shelf You do that too? Just as well, my sack is getting full.
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I don’t have any specific lore to back it up, but I suspect there probably weren’t Champions for ALL the races in the Green Age, just the powerful or populous ones.
If the list of races that had Champions is the full list of all Green Age demihuman/ humanoid races, that would mean that all currently extant demihuman/ humanoid races (except for Kreen and Gith) had to evolved or mutated from animals or: Humans, Halflings, Giants, Pterrans (maybe), Elves, Aarakocra, Dwarves, or Tari.
That seems unlikely, even if we assume that some races, like the Nikaal, have emmegrated to the Tablelands from far away.
It seem more logical (if not strictly supported by canon) to imagine that there were other Champions in other parts of the world for other races or that those races were too minor to have designated Champions.
Ssurrans, for example, may have been a little known offshoot race of Lizardfolk in the Green Age and Rajaat either figured Keltis would get them too, or just assumed they would be powerless to stop the Return to to the Blue Age and would die off.
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Teenage mutant ninja gith-lings?
I know I’ve always run it as Rajaat specifically targeted two types of races for the Cleansing. He went after races that could potentially stop him (powerful in magic or psionics) and races that had a high population (high birthrate, lot of people do to longevity).
In my world the Pristine Tower was altered by Rajaat to not just focus magic, but absorb power from the sun directly and from the death of every cleansed being - but that death power could only be gathered from species created by the Pristine Tower. This is also why he was so powerful when he escaped, he had thousands of years of energy just soaked into the Pristine Tower he could call on. I had other Champions, the ones we know about are just the ones that were most active in the Tablelands in recent history, but nowhere near 1 per sentient race.
Back to the OP, Gith were degenerate Githyanki as detailed in the Black Spine adventure in my world.
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Building on your explanation, maybe they were very rare at the time and definitely too primitive too be considered as a threat to rajaat future plans, and he could have easily eradicated them at his leisure once all the other more troublesome races have been disposed of.
This could also explain why they are much more numerous in the present, as after the cleansing wars there was a lot more room for them to breed and expand without competition as most of the civilized race were either eradicated completely, or has suffered a massive decrease in population from attempted genocide or the effects of rapid desertification due to the unrestrained defiling.
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I will be adapting the Goodman Games version of The Lost City to my Dark Sun campaign, and deep in the caverns below the city there is one Illithid still working there, who works for Zargon to poison the water with mind altering mushrooms… I will add a Gith faction to the mix that will be in opposition to the illithid that the players can ally with if they choose to, or be aggressive with which ever they choose, but it will at least alert them to the presence of a mind flayer at some point still alive on Athas…
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