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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.

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  • PAM won't talk to you - do you mean she can't be reprogrammed?
    – Joachim
    Sep 2, 2019 at 14:18

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You can try to get banished from the Institute.

Under most circumstances, becoming enemies with the Institute immediately fails Underground Undercover and any active, related Railroad quests and starts Burning Cover instead.

There are a few ways to get banished, but the following one seems appropriate:

  • Kill any named Institute personnel.

This seems to be the easiest way for your purposes, especially since you almost did this anyway :)

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