It's still says "Continue working with Father".

The problem is that Father wants me to kill Desdemona and the Railroad. I talked to Desdemona and told her about it and she just told me to continue working with Patriot in the Institute, but that's the Underground Undercover quest which still says "continue working with Father".

So what do I do?

I think I read somewhere that you need to complete the "Mankind-Redefined" quest and the "Mass Fusion" quest.

Of course, if you don't want to do that, you could just start shooting institute scientists. I think that will accelerate the Railroad plot by starting a new quest called "Burning Cover."

I believe that if you are a certain point in the Institute's quests, you can initiate the objective after "Continue working for Father". I believe that if you're far enough to get the kill request, then you should be far enough to progress Underground Undercover. First, talk to Desdemona and warn her what you've been ordered to do. I don't know if this actually does something, but it's what I did. Then go back to the Institute. If you run around a bit, a generic gen 2 synth will walk by you and tell you that Z1 is in your room at the Institute. Go to your room and talk to him. If you can't find the synth, you could probably just go ahead into your room.