The stakes are raised during this second Institute mission, where Father wants you to track down and recover a number of Synths who have escaped to Bunker Hill. This means assaulting the monument and, if Father had his wish, resetting the Synths. While this mission will test the waters on your faction allegiances, your upcoming actions won't burn bridges. If you'd like to warn either or both the Brotherhood of Steel or the Railroad, go ahead. We opted for the latter.
After speaking with father, meet up with a Courser near the edge of Bunker Hill. He'll start off as your ally, but if you decide to free the Synths, he'll become your enemy. Your current allegiances will determine how much you'll be fired on. You could be fortunate enough that all you deal with are a couple turrets. Once you've made it inside the monument and past the basement trapdoor, you get to make your decision on the fates of the Synths.
Rather than resetting them for Father or killing them to impress the Brotherhood, we opted to free the Synths to gain some brownie points with the Railroad. It was of minor consequence when meeting up with Father after the mission. He can be found at the CIT Ruins, at the top of the CIT Rotunda which you can reach by going into the ruins. After you explain yourself to Father, the quest will conclude.