WARNING POTENTIAL SPOILERS AHEAD:

So i just did the "Insitutionalized" quest and decided to not work with Father(Shaun) and i haven't got a new story quest, so I'm quite worried i might have finished the game without even noticing, can someone please help.

Im at the same point in the story right now. I guess you just have to either work for the institute or go to the different fractions and help them destroy it.