SPOILER BELOW...although, it's been ~6 months since the game came out, so at this point, most reasonable fandoms would have proclaimed the spoiler period well over by now...
In any case, the Battle for Bunker Hill seems to be the draw point for Institute vs. Brotherhood vs. Railroad. You have to pick a side here if you're rooting for one of those three factions (the Minutemen don't have a stake in this battle, so it doesn't matter to them about the outcome). You don't have to fight in the battle, per se (I didn't...I sat back and watched it unfold), but you still have to decide what to do with the synths in the basemant once the above-ground & below-ground battles end. If you let the synths go or port away without a decision, you anger Father and the Brotherhood once you go back to either side. If you kill the synths, you anger the Railroad if you go back to them.
This quest the part of the game I was most dreading, personally, as I wanted to find a peaceful solution for all sides, but the game designers don't let you do that. Someone has to go if you make it to this quest and accept it.
Personally, I'm hoping for a future DLC that changes the program just enough that a negotiated peace might be an option for the four factions. After all, what's the point of a high Charisma if you can't use it to get people to listen to reason and change their minds???