I have successfully restored the archive and completed everything and the quest tell me to hand over the calcuceus but there is no NPC to hand it over to.

When first entering the archive I cleared the area of enemies without reinforcements from aunties or the order which might have caused this specific bug.

I was experiencing the exact same issue, under the same circumstances as well.

I ended up figuring out the issue, as you just have to enable the elevator for reinforcements to come down. I hope that helps.

I appreciate it but I had already activated the elevator, pretty sure I sequence broke it by doing that.

Did you interact with the nearby intercom to actually summon the troops? In my prior screenshot, it is roughly just right of center.. by the break in the guardrail. There really should be quest markers for activating the lift.

I'm having the same problem. Don't know what to do. Cant reload to before I entered archives. 

I can't interact with anything by the lift unfortunately.

I am having the same issue. I can't hand over the Calcaduceus because there is no one at the quest marker to hand it over to. As a result I can't do any more faction quests. I suspect it's because I cleared out the archive on my own. 

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.

This exact scenario is happening to me, so annoying. Spent ages trying all sorts of interactions, running around back to the two factions, completely clearing out the under city etc. 

The best I can find is people saying to call the troops from the elevator, but that has obviously already been done as that locks the actual archive sections.

Seems i'll just have to plod on and hope for a bug fix and come back to this and the main quest later.

I'm having the same issue, and unfortunately it means I don't have an alliance for the final mission. This needs fixed. Hopefully they will see this and do something about it soon. I'm putting off finishing the game because of it.

Same. It's the only thing I have left before the end game and I don't want to proceed without completing it!

Same issue:  took the Archive solo, after that I try to complete Auntie's Choice missions, it starts dialog with Auntie, but it interrupts. I cannot use HQ elevator, I cannot complete the Order missions - it makes Auntie's Choice aggressive.

Facing the exact same issue. I ended up clearing Spireton alone, but then going to the Archive via Newton. Cleared it myself without help, then I went back and did all the parts of Equitable Arrangement. After I fixed UENIAC, there was nobody waiting for me to take the Caladuceus. 

I tried fast traveling to Spireton and some Archive soldiers appeared and ran to the lift, but the door was still locked. I unlocked the lift from the Archive side but still nobody is coming up to advance the quest.

Now I guess I need to decide whether to wait an indefinite amount of time for this bug to be fixed (it's been a month since this thread was created) or just do the final mission alone so I can finish the game.

Still no updates :(. Can't finish game and start new session.

Super frustrating. There's gotta be a patch for this game breaking bug. What's going on Obsidian?

In the 1.0.6.0 Patch Notes it states: 

"The player is now able to continue the quest "An Equitable Arrangement" if they have captured The Archive independently from allying with either faction beforehand."

I still cannot find where to progress the quest or who to talk to.

1 hour ago, Brosif3r said:

In the 1.0.6.0 Patch Notes it states: 

"The player is now able to continue the quest "An Equitable Arrangement" if they have captured The Archive independently from allying with either faction beforehand."

I still cannot find where to progress the quest or who to talk to.

I'll hop on to my old save and see what happened. I wonder if it'll work with mine because I technically got them to compromise while taking the archive.

I still can't finish the game.
Yes, they fixed AC dialog, thank you. She is ready for dialog with Order, but said that I still need to complete some missions for Ruth.
When I talk to Ruth - she takes the magic stick and AC becomes angry. I finished two missions for Order (chemical manufactory and space station), and now I need to kill AC. So, no negotiations, no dialog lines.

It's fixed for me, but I'd already completed all the Order quests and was stuck at Auntie's Choice.