Sole survivor goes through mass fusion with the BoS, but at the end X6-88 EMPs Proctor Ingam. Paladin Danse is controlled to let the sole survivor to enter the prydwin after becoming enemies. At the meeting the weapon scientist suggests using Paladin Danse to disable the BoS main defenses. 1st: it cannot be completed before meeting with the institute heads. This is the key to conquering the BoS instead of exterminating them.
This mod is a massive undertaking and welcomes any who want to help.
My minuteman army is loyal, the Railroad can be reasoned with, and I can conquer the BoS while taking over all of their weapons, munitions, and armor. I am the god damn leader of the institute, so fall in line and quit giving me one choice.