If you choose the Minutemen as you faction, after you beat the Institute and get the main quest ending, Preston Garvey will then tell you that you need to also take out the Brotherhood of Steel to restore order in the Commonwealth. After preparing artillery throughout the Commonwealth, you surprise attack the Brotherhood's ship, the Prywden. but they have one last attack in them. You have to defend the Castle to defeat them. The battle is epic, and a nice payoff to the story. I wondering if there is a way to delegate between the two sides though. The problem for was, that I went through the Brotherhood's questline, but betrayed them when Maxson tried to force me to kill a friend. I wonder if I didn't betray them if I could delegate. As it stood, if I tried fast traveeling to the ship I would immediately be shot at, so I guess I won't know unless I play again. But nonetheless, still a fun and epic battle. Check it out!