My personal take is that t'leth was/is a seeder ship, Piratez lore implies that the SG empire primary means of long distance interstellar travel is black hole "gates". Go in one black hole come out another in some other part of reality. Given the need for such assistance it can be presumed that SG grav drive while fast is not capable of high FTL speed. Also the expansion of the gate network probably requires slowboating the parts for another gate to the far end on grav drive alone.
Given the slowboat needs of the gate system the obvious means of expansion is semi autonomous seeder craft. Send out some in your given direction of expansion to build gates and seed worlds with compatible biospheres. For some reason t'leth crashes and while it survives, it no longer has the capacity to remove itself from the seabed, and probably some significant control system damage. What it does have is stocks of biomass, energy and time to spare.
It makes some adaptations to the standard sectoid to handle its new ocean location and sets about slowly trying to do its job, seed a world. Either programing flaws or the damage of the crash render the orders only partly right so it only seeds the deep oceans. Lack of elerium or some other critical elements prevent its full repair so it makes do with what it can make, Zirbite. A signal for aid is either impossible to send or never sent due damaged/flawed programing. 65 million years pass while it toils, very slowly, unseen beneath the ocean. Aquatoids, Deep ones and the rest come into being.
SG turns up, finally, does there thing, and in the process notices t'leths presence. Salvage or repair is deemed unresonable or technically infeasible for something hugely antiquated. But its not useless either, it holds sway over some 70% of the surface area of the planet and doing something moderately productive. So they dont shut it down.
Then the divergence on if X-com wins or not. If they do win the dying brain sends it's revenge commands to tl'eth. T'leth acts on these new instructions and musters up a war against the surface. X-com failure on the other hand leads to it doing the same things its been doing for 65 million years, populating the deeps.
600 years pass, the lack of tleth never getting war orders results in the slow spread of the deep ones eventually coming into conflict with the surfacers on there own with little direct influence, everybody needs space when things get crowed, so they go looking for the neighbors spot. Being almost exclusively underwater civilization leads to some significant environmental influences on there tech base. Gunpowder, explosives, and basic electronics don't do so well in fathoms of saltwater. Your also limited in your materials ability, no hot forging down here, unless you wanna stick your face in a volcanic vent. Muscle power and beasts of burden/war still do work however. So they have muscle powered weapons, some nasty pets, and a few sonic gifts/relics from the dreaming city.
Piratez deep ones are the barbarian fringes of the t'leth civilization come looking for greener pastures. Raiders but from an aquatic/wet tech base.
