The Nuclear Option (Railroad)

The Nuclear Option is a Railroad main quest and Fallout 4 achievements and trophies in Fallout 4.

Detailed walkthrough
After finishing Rockets' Red Glare, Desdemona will give this quest to the player. You need to fast travel to the Institute and enter the central elevator. Once you get to the relay room, speak to Z1-14. He will tell you 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 you 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 -- you will arrive at the Institute Bioscience wing. After fighting your way though this wing (scientists, synths and the synthetic gorillas will be hostile), you will enter the main area of the Institute, where you will 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 you 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. You 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 you a code to shut down most of the hostile synths remaining in the main area of the Institute. You also issue the evacuation order on this terminal, which allows Z1-14 and the other rebel synths to rescue non-hostile synths.

You will then fight through the last remaining hostile synths in the Advanced wing (including two legendaries) on your way to the reactor terminal. After disengaging the reactor lockdown on the terminal, enter the reactor and plant the fusion charge where you placed the Beryllium Agitator in the quest Powering Up. Tinker Tom will then teleport you and Desdemona back to the relay room, where Tom has found Shaun (the synth child, duplicant of Father). The player must choose between taking the child with them 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.

Bugs

 * Teleporting into the Institute wearing a power armor helmet with the targeting HUD mod, with this quest active, makes the player partially hostile to the Institute, denying the player 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.
 * The quest may be completable with copious abuse the of console command.
 * The player is 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.
 * If the quest is never started (for example, if decided to destroy the Railroad instead), the rebel synths on the mining floor will still be there, non-hostile, standing and doing nothing forever.
 * After detonating, some players might experience the screen fading to black and eventually will be stuck loading the next cutscene. You use the console to relocate yourself to another location with the command (in this case, Red Rocket) and continue the game. Then type  to update the Mass Fusion building cell.
 * If you dismiss a companion while in the Institute, they never return home. Tested on PC by dismissing Deacon in favor of X6-88 while in the SRB wing. After, finds him standing there in SRB.