With the Brotherhood of Steel merely steps away from finally taking the war to the Institute's doorstep, an obstacle remains in the way, as seen with The Railroad, in which their ideologies to save the synths is in stark contrast to the Brotherhood's ultimate mission, and as such, must be destroyed.
Lancer-Captain Kells will request for the Sole Survivor's presence, in which he will reveal that the Brotherhood of Steel have decided to eliminate The Railroad, as their fanatical ideologies are considered detrimental to the Brotherhood's cause and mission. The Sole Survivor will then need to travel to Railroad HQ.
Merely accepting the mission turns the Railroad permanently hostile.
Upon arrival, the player has to fight their way in, first killing Doc Carrington in the church above. Then they have to make their way through Railroad heavies down to the headquarters, open the way into the secret tunnel with an explosive charge (simply activated), and then enter the HQ.