The Nuclear Option (Brotherhood of Steel)

The Nuclear Option is the final Brotherhood of Steel main quest and an achievement/trophy in Fallout 4.

Detailed walkthrough
After dropping into the hole made by Liberty Prime (completing Ad Victoriam), the Brotherhood insertion team will find itself around the corner from the teleportation room where the Sole Survivor first entered the Institute. Elder Maxson will hand out an explosive charge to place on the Institute reactor. Proctor Ingram stays behind to get the teleporter working, and the rest of the team proceeds forward.

The Sole Survivor must go through the old Robotics wing, now a ruined section of the Institute, eventually coming out in Bioscience. If the Sole Survivor has not retrieved the experimental serum for Virgil yet, they should do so now as it will be their last chance.

Once in the main section of the Institute, they must clear it of enemies. Once done, they must go to speak to Father. Father can be persuaded with a Speech check to reveal the password to disable a part of the synths that protect the Institute. Once finished, they can do as they wish with Father, and issue the evacuation order if they wish to. Afterwards, they must enter Advanced Systems, then clear the section of enemies, and get to the reactor. After doing so, they must activate the terminal, activate the radiation sweep, and then disable the reactor's shielding. Then, they must plant the explosive. They will then be teleported out of the reactor section. Ingram will explain that Shaun, the synth child, showed up. The Sole Survivor must decide what to do with Shaun, and must then step into the molecular relay.

Afterwards, Maxson will tell them that the honor should be theirs to activate the explosive. After doing so, Maxson will tell them to return to the Prydwen and the quest will be completed.

Bugs

 * After blowing up the Institute one may find themselves unable to talk to Elder Maxson to continue the quest, or he may be absent. For the PC, open the console and use commands, and then  to teleport Elder Maxson to the player's location.
 * One may not need to use, just &.
 * Entering and exiting the FEV lab may cause several synths to become allied to the Brotherhood and attack other synths.
 * Quest may become stuck on "Speak with Shaun" with no way to move forward without using the console.
 * (taking Shaun) or (leaving Shaun) will fix this issue.