Tactical Thinking

Warning:This quest will make you the enemy of the Railroad and will require you to kill Deacon as well. If you still want to preserve the Railroad while still being loyal to the Brotherhood, you can skip this quest by continuing with The Institute quests up until you reach Mass Fusion. Once you trigger the quest, you'll have the option to Inform the Brotherhood. Doing this will trigger the BoS quest, Spoils of War which also takes place in the Mass Fusion Building. This will give Proctor Ingram a new dialogue option related to the new quest. (Spoils of War makes you a permanent enemy of the Institute) Tactical Thinking will still remain active and incomplete, as long as you don't talk to Kells.

Tip: Before talking to Kells, make sure to tie your loose ends with the Railroad and maximizing Deacon’s affinity to you so you can get his perk before needing to kill him.

Kells will give you the order to kill key Railroad personnel. In the other hand Ingram will also inform you hack PAM's terminal. You'll need to head to the Old North Church and assault the base with your Brotherhood allies. Once inside the church, you have to kill the key Railroad personnel. First you have to kill Dr. Carrington in the main chapel.

Next, head to the catacombs then activate the detonator to breach the brick wall. Now you have to kill all the remaining members in the HQ. After killing everyone in the Railroad, access PAM's terminal then load the PAM Decryption Program then start her reset. Once done, report back to Kells to complete this quest.

Extinguishing the Railroad's lantern.