I wanted to go through the Railroad and Brotherhood quest as much as possible without killing each other before beating the game with the Minutemen. I can't start the Minutemen quest until I've failed Underground Undercover. So I killed a scientist but then nothing happens. I found out you need to complete Tradecraft, which I did. I tried to complete all the quests that come after that, but Mercer Safehouse was glitched because I have the Tactical Thinking quest open and P.A.M. won't talk to me. Since those quests aren't technically Tradecraft I don't know if they matter.
Is there a way to fail Underground Undercover under these circumstances, and is there a way to fix P.A.M.?
I also found a bug where you can't talk to Desdemona, and that may be part of the issue.