Possible Fallout 4 glitch (or maybe I’m just stuck): On the mission “Underground Undercover” the quest seems to be stuck on “Continue working with father”. I’ve finished “Powering Up” and moved on to “End of the Line” where I have to kill Desdemona. Instead I warned her that Father wants her dead, and she basically just said continue working with the Institute. There’s nothing else for me to do, considering I want to keep working with the Railroad.
so what do I do now?
After Powering Up, in the Directorate Room an unnamed Synth quietly approaches you to tell you about your quarters flooding, go there and it triggers the next step in the RR questline. Don’t talk to Father, make sure you talk to that Synth. He’s really easy to over look!