The Nuclear Option (Railroad)

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

Detailed walkthrough
After finishing Rockets' Red Glare, Desdemona will give this quest to the Sole Survivor. They need to fast travel to the Institute and enter the central elevator. Once arriving at the relay room, speak to Z1-14. He will tell the player character to kill everyone in the relay room (two synths and three Institute scientists). After everyone in the room is dead, Desdemona, Tinker Tom and several other Railroad members will teleport in through the relay. After talking to Desdemona, the player character will need to enter the old robotics room, a previously inaccessible door to the left of the central elevator.

After passing through this area, which includes dozens of synths, a few laser turrets and a sentry bot, the player character will arrive at the Institute Bioscience wing. After fighting their way though this wing (scientists, synths and the synthetic gorillas will be hostile), enter the main area of the Institute to join in the fight with the rebel synths from Underground Undercover to clear the area.

Tinker Tom will then come on the loudspeaker and ask to use Father's terminal to unlock the doors to the reactor. Enter Father's room and simply use the terminal to unlock the doors. One can now kill Father or leave him on his death bed with no consequences. Talking to Father beforehand and passing two speech checks can give the player character a code to shut down most of the hostile synths remaining in the main area of the Institute. Also issue the evacuation order on this terminal to allow Z1-14 and the other rebel synths to rescue non-hostile synths.

The player character will then fight through the last remaining hostile synths in the Advanced wing on their way to the reactor terminal. After disengaging the reactor lockdown on the terminal, enter the reactor and plant the fusion charge where the beryllium agitator was placed in the quest Powering Up. Tinker Tom will then teleport the player character and Desdemona back to the relay room, where Tom has found synth Shaun. Then choose between taking the child or leaving him behind.

Everyone is teleported out of the Institute to the roof of the Mass Fusion building, a safe distance away from the fusion charge's blast radius. Simply press the detonator button on the rooftop and watch the large explosion wipe out the entire Institute. Desdemona remarks that there will be retaliation from the Institute forces that managed to escape, however the Institute will never recover from the destruction of their HQ and research.

After some time, Drummer Boy in the Railroad HQ will inform the Sole Survivor that the Vertibird is ready for use, and hands over three Vertibird signal grenades. More grenades can be purchased from Tinker Tom.

Bugs

 * Teleporting into the Institute wearing a power armor helmet with the targeting HUD mod, with this quest active, makes the player character partially hostile to the Institute, denying them access to the elevator, and not spawning any Institute NPCs except Father.
 * Reloading a save from before entering the Institute, and taking off the targeting HUD mod is recommended.
 * It is possible to finish the quest without loading a previous save, by just backtracking all the way UP (without the elevator) via the way in which the quest wants you to go DOWN later on (through "BioScience" and "Old Robot") But you will need a jetpack equipped to get through a hatch in the roof one time.
 * The quest may also be completed with use of the console command.
 * The player character was earlier given the option to deposit weapons for the synth rebels, however upon commencing the attack, it is evident that the cache has been disregarded, and is seemingly impossible to gain access to again.
 * After the Institute detonation, the player character might experience the screen fading to black and eventually will be stuck loading the next cutscene. Use the console to relocate the Sole Survivor (in this case, Red Rocket) and continue the game. Then type  to update the Mass Fusion building cell.
 * If a companion is dismissed while in the Institute, they never return home. Afterward, finds them standing there in SRB.
 * When Tinker Tom teleports the Sole Survivor back from the reactor after they have planted the fusion charge, they may be teleported not to the relay room, but to the Mass Fusion executive suite. The detonator will be placed, but it can't be interacted with (and, as it happens, Institute quest Mass Fusion may commence). The only way to fix this is to use the console to get back to The Institute (e.g., ), head back to the relay room, and talk to Tom and Shaun. (It is possible this is caused by not having done a quest to acquire the beryllium agitator.)
 * When Z1-14 is teleporting the Railroad into the Institute, if one enters the teleporter, it is possible for the player character to be immediately teleported to the Mass Fusion Executive Suite, where the detonator has yet to be placed. The only way to fix this is to use the console to get back to The Institute (e.g., ), head back to the relay room, and talk to Desdemona.
 * After clearing the main area and Tinker Tom finishes announcing the lockdown needs to be raised, the central elevator may disappear while leaving the door open. If the call buttons are pressed, it will deny access. Jumping down the elevator reveals the doors are shut at the bottom. A work around is to use the “tcl” command to move through the closed elevator door.