I'm also experiencing the same problem. My order of events were enter the archive, companions warning me I should get an alliance to which I say sabotage first alliance later (I mean this option is why I think I still should be able to progress), activate the elevator, handle the alliance/negotiations, capture spireton. Now the elevator controls, the intercom next to it and the npcs at spireton are uninteractible. If I clear the archive game counts it as a solo takeover and even after restoring the archive I am left at the same place with the companions telling me I have no allies if I choose to carry on with the game.
