Tau Ceti Flowering: Horrors visited upon neighboring systems must never be repeated. Therefore: if it means the end of our evolution as a species, so be it.
– Caretaker Lular H’minee, “Sacrifice : Life”
Thus speaks Caretaker Lular H’minee, setting the stage for why the Usurpers have to be stopped. The Tau Ceti Flowering can be read as another Planet – not Chiron, but a planet built on the same specs – achieving sentience, and the consequences following that event. We know from the fact that neither the Usurpers nor Caretakers are gods (albeit both mechanically overpowered) that the Flowering happened without anyone at the helm. The exact nature of the horrors inflicted upon the neighboring systems is not known, but it is safe to assume from the two alien leader quotes that it would be bad even if it only happened to one singular system. The fact that it can reach across the stars only adds to the horror.
To say that the Caretakers are dedicated towards stopping transcendence from happening is – just as with the Usurpers – a massive understatement. It is their entire reason for being, both on and off Planet, and thus everything that stands in their way has to be removed. The most immediate concern is of course their Usurper counterpart, but given that humanity too seeks to transcend (albeit without quite knowing it yet, busy as they are trying to survive), the prospects of peace are slim. History is in the making, and it has to be stopped at all costs. The source of the leader quote – Sacrifice: Life – speaks to this.
This state of things explains one of the most misunderstood mechanical aspects of the expansion. The Caretakers, alone among all factions, cannot complete the secret project Ascent to Transcendence. Mechanically, this simply means that they cannot win a transcendence victory, which many have read as a bug in the game. It is however not a bug, but very much a narrative feature: it would make very little sense for a faction to dedicate itself to stopping something from happening, only to then be the ones to see it through to completion. Quite unlike the Cultists, the Caretakers are not willing to backpedal themselves to victory.
The name “Caretakers” carries with it benevolent connotations, especially when contrasted with its Usurper counterpart. To take care of and preserve something is inherently to ensure that it is given an opportunity to grow and prosper; there is an element of Heideggerian sorge to it. To care is to be involved, and to be willing to take action to ensure a positive outcome. However, it also carries with it the connotation inherent in the phrase “take care of the problem”, that is to do whatever is necessary to see that the problem goes away. In the case of humanity, the problem is not seen as a diplomatic issue to be resolved through reason and arguments, but rather akin to weeds having intruded into a garden. As Zygmunt Bauman wrote: there is no inherent difference between weeds and flowers, other than the decision that a particular plant belongs to either category. The care shown for flowers is fully compatible and complementary to the violence inflicted on the weeds; in order for the flowers to live, the weeds have to be purged and removed.
It is left unsaid whether the Caretakers have taken this role upon itself with regards to Planet only, or if it is something they do with regards to all members of the Manifold. The fact that the Usurpers were on their way to Chiron in particular lends more urgency to this part of the universe, given that failure here means failure everywhere. It is not unthinkable, however, that the same role extends to every other planet with similar characteristics, and that it was mere cosmic coincidence that the conflict happened to occur right when humanity made their appearance. Given that space is big and that it is impossible to be everywhere at once, the Caretakers might have taken turns gardening each planet for some hundreds of years before moving on to the next one, ensuring that everything goes according to plan. It is quite possible that the base game was simply a slightly alternate universe where circumstances dictated that the alien civil war emerged on Chiron a mere half millennium later than in the expansion; just in time to be befuddled by a transcended humanity figuring out what to do with a planetary frame of reference.
There is one last unanswered question, and that is whether the aliens build the Manifold or not. There are cases to be made either way. The fact that the Usurpers knew in the first place where to go to make their attempt at godhood suggests that the aliens possess some sort of advanced knowledge of Planet and its siblings; it is possible that they built the Manifold long ago and now simply take care of it. However, it is equally possible that the aliens found the Manifold and harnessed its power to become what they are today, much like the humans on Planet. The sudden Flowering on Tau Ceti thus presented itself as a new opportunity on other Manifold planets, one that could be usurped (pun very much intended) for new and untold purposes. Speaking to this second possibility is the fact that the aliens, too, discover the in-game technologies of Secrets of Alpha Centauri and Secrets of the Manifold. It is unlikely that the aliens went through all the trouble of building the Manifold for some grand purpose, only to forget it a while later; it would be inscribed into the very cultural core of the civilization.
Unless, of course, the civil war had been going on for so long that those ancestral builders have become akin to aliens themselves, possessing vastly greater knowledge and resources than the war-torn descendants remaining today. Not, come to think of it, unlike how the human survivors setting up that first base on Chiron relate to Earth: small remnants remembering the outlines of their home cultures, but not having access to it in their immediate physical proximity.
The Progenitor backstory does leave room for speculation, and I suspect a transcended humanity (from base game and expansion both) would be eager to find out the specifics.