I chose to become the leader of the institue, but unfortunately they will all die, because Owen Newton (I think that's his name) won't move when I'm supposed to follow him because of two scientists who locked themselves in and cut the food supply.
I noticed that once I killed off all the other factions - except for the Minutemen that consists of one guy - I still had two quests that I shouldn't have. One was to set up a MILA for the Railroad, and the other was something BoS related.
