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 BoS 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 gotten Virgil's Cure, they should do so now as it will be the 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. 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, and activate the radiation sweep, 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 showed up. The Sole Survivor must decide what to do with Shaun, and then must 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.
 * The player can sometimes be unable to fast travel after killing themselves and reloading on the Mass Fusion building before detonating the bomb.
 * After completing Ad Victoriam and entering the Institute, Elder Maxson and the rest of the team may not show up. It will not be possible to receive this quest from Elder Maxson but one can enter the Institute, but they will attack once the player steps out of the elevator.
 * 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.
 * If Father was killed before confronting him during the quest, his body will spawn sideways in mid air.