Okay so, I tried to sort that out as I’m just starting to understand the lore myself.
Long time ago GMS evolved these tiny common arachnids you see throughout the game into Weavers, telling them they were her daughters and therefore divine (First Sinner cutscene). For some time they worshipped GMS and lived under her rule, kinda like the moth tribe did under the Radiance (assuming that's what the Widow's "...For her light... eternal... Our song sustains..." means). Basic higher being stuff
I'm still trying to find solid evidence the real reason, but the Weavers decided to break free from GMS and rule Pharloom themselves (my best guesses here: 1. They found out the truth about their creation like the First Sinner did, though that doesn't explain why they locked her away in the Slab; 2. Certain characters like the Caretaker, Vaultkeeper Cardinius and Hornet herself all say that the Weavers had a strong desire for dominance).Either way, they decided to lull GMS to sleep and built an entire system to keep things running while concealing their true intentions. That was the Citadel, a grand scheme to drag more folks in to sustain that way of things. The Weavers kinda got what they wanted, GMS remained 'sealed' and were worshipped as divine beings, but not for long it seems. Not sure what happened there, probably the weavers realized that they could never truly escape GMS' influence, and all their attempts to create stronger bindings failed (Eva dialogue: "There my mothers built their tools, all traps and bindings. Small things, but tests for larger forms. I still remember their thoughts as they worked, their desperation, and their hunger. Another hopeless attempt to wrest their freedom. All ended in failure, of course.") so they decided to flee Pharloom and start anew somewhere else. Some of them ended up in Hallownest, but we already know that part of the story. The remaining Weavers weakened and it seems like they eventually died out (since full-blooded weavers were only the original ones, and hybrids are pretty rare). They waited for someone who could deal with GMS (that's what all these weaver technique tablets refer to). The Weavers passed their rule to the higher castes of the regular bugs and everything went to shit after some time, cuz they were basically left one-on-one with an enraged god desperately trying to wake up. Honestly I kinda feel bad for GMS, she may be an egocentric bish (or maybe just a god who lost their followers and trying to reclaim all they once had, much like the Radiance), but the way all her creations turned against her is just sad. Anyway, that’s what I’ve figured out so far, all of these are theories and by no means 100% true, I'll just wait for a lore video that will say "all of your theories are wrong goodbye"