When given the choice on siding with what faction to take the archive with i initially did the quests for AC after finishing the last quest "Mysteries of the Mental Modulators" you're give an opportunity to speak to Auntie Cleo not wanting to making a big commitment (as I wanted to negotiate peace between the two factions) i exited dialog and then started the order factions quests after finishing them and speaking to Ruth about having an alliance it say to speak to Auntie but my only option is to speak to the 2 VPs about only siding with Auntie

i have this issue too....can't believe such a major bug exists in this game.