Take your station in the Vertibird at the minigun and Tinker Tom will attempt to pilot the ship past the defenses in a ruse. Enjoy the scenery of the Commonwealth as you travel! Once arrived on The Prydwen, donning the Brotherhood apparel given to you by Deacon will allow you to move about freely and speak with Brotherhood members. You can attempt to talk your way to planting the explosives but it is likely violence will break out at some point. Progress to the main deck of The Prydwen and set the 3 explosives where the Pip-Boy indicates.
After setting the charges leave from whence you came, fighting your way through the Brotherhood, and be prepared for a a lengthy firefight. Loot the bodies along the way for valuable Fusion Core that can extend your fight if your wearing Power Armor. You will have an opportunity to put an end to Elder Maxson as well as the rest of the Brotherhood leadership. Exit to the flight deck and board the vertibird for escape. Once clear, the charges will be detonated, bringing an end to Brotherhood. Tinker Tom will drop you off on a beach nearby while he stashes the stolen vehicle. Return to the Railroad and speak with Desdemona, who will give you the Railway Rifle Mod.