The Nuclear Option (Minutemen)

The Nuclear Option (Minutemen) is a quest in Fallout 4.

Detailed walkthrough
Talking to Preston Garvey after having defended the Castle from the Institute's retaliatory attack will initiate this quest, provided the Sole Survivor has a total of at least eight settlements under their control.

Otherwise the quest Form Ranks will be given instead and must be finished first. Once Garvey considers the Minutemen ready to take on the Institute, he will advise the Survivor to speak to Sturges, who has meanwhile completed his analysis of the Institute data they brought back earlier.

Sturges can usually be found in Sanctuary if he wasn't sent somewhere else. He notifies the Survivor of a possible backdoor into the Institute: an old cooling water tunnel system. He then gives the player a holotape with which they can reprogram the Institute Relay in order to teleport in Minutemen reinforcements. He also mentions insistent radiation warnings about the area you need to traverse, so prepare yourself accordingly.

Opening the map once Sturges finishes his briefing will lead you to the C.I.T. ruins. However, the true destination is only shown by your compass and will eventually lead you to the flooded entrance to the cooling water tunnels at the river bank directly south of Ticonderoga. From there it is only a short walk until the Sole Survivor reaches dry ground again, so no Aquaboy perk or Mirelurk cake is necessary when opting for power armor.

Once you are underground and out of the water, there is an advanced-locked terminal to the left that opens a small room with minor loot. To the right you will find a keypad that needs to be interacted with in order to clear the path forward. Proceed through the large, partly flooded pipe that runs below the small room the terminal opened. The path is mostly linear and crawling with ceiling-mounted laser turrets, mole rats and feral ghouls. It also involves trudging through irradiated water most of the time, so hopefully you heeded Sturges' warning.

Eventually you will reach an elevated walkway with a hard-to-miss expert-locked terminal. From here on the Survivor will encounter hostile synths, two of which can be ambushed through a hole in the wall right next to the terminal. If your hacking skills are insufficient to open the door, proceed along the tunnel until you reach another door. Make your way through the ruins, picking up a Fusion core from a generator, an Overdue book from an abandoned classroom and several pieces of combat gear along the way, among them a Stealth Boy. Once you arrive at the room where you saw the first synths through the damaged wall, continue through another large pipe on the lower level into the Institute proper.

The pipe brings you directly into the Relay control room where you need to load the Institute relay targeting sequence holotape into the marked console. Doing so will teleport in Garvey, Sturges and several Minutemen. Talk to Garvey and accept the Fusion pulse charge before you take charge of the attack on the reactor. Fight your way through Institute forces, turrets and a Sentry bot, the latter of which can be destroyed before it powers up if you are quick enough. After reaching an iris-like hatch in the floor and jumping down to the next-lower level, pick up another fusion core from the nearby generator before proceeding to the Bioscience facilities. Dispatch all hostile synths and beware the synth gorillas that get turned loose, should the Sole Survivor venture too close to their compound.

The next area contains a lot of hostile synths including several Coursers that usually attack under the cover of their Stealth Boys. The Survivor will also encounter at least one named legendary synth here. Once all enemies have been taken care of, Sturges will direct you to the Advanced Systems department, only to tell you that it has been locked down and needs to be opened from the Director's personal terminal. Use the large central elevator to reach Father's quarters where he lies dying. Talk to him if you feel like it; convincing him to help you by passing an easy charisma check will provide the Sole Survivor with the password for his terminal.

Alternatively, simply hack the novice-locked computer in order to use it to lift the security lock down. You can also make the rest of the mission easier by shutting down some of the synths, as well as opt to fulfill the optional objective by engaging the Evacuation Protocol BD-2, which is highly recommended if you plan on continuing your work with the Railroad. If you don't evacuate, the entire Railroad will turn hostile as soon as you meet them again. Also, Garvey will hate not giving the evacuation order. Once you are done, head for the Advanced Systems facilities and the reactor.

Securing the reactor involves a tough fire fight in close quarters. Again you will encounter two named legendary synths that wield powerful weapons and carry the Reactor Terminal Password. Make sure to shut down the reactor and initiate the radiation purge before you enter to place the fusion charge. Talk to Garvey and let Sturges teleport you to the Relay control room where the Sole Survivor encounters synth-Shaun. Deal with the kid as you see fit, then talk to Sturges. This is your last chance to return to collect whatever you might have missed in the Institute. Choosing to abandon synth Shaun will prevent the Sole Survivor from receiving Shaun's unmarked quests, making the Wazer Wifle unobtainable.

Once you are ready, tell Sturges so and step into the Relay. You will then be teleported to the roof of the Mass Fusion building. Pressing the detonator in front of you will blow up the Institute's reactor and initiate the epilogue cut scene. Talking to Garvey afterwards finishes the mission. Should you have made enemies with the Brotherhood of Steel by this point, the next mission With Our Powers Combined will usually start as soon as you get in Garvey's dialogue range again.

Bugs and glitches
(Spoilers ahead.) If you decide to keep both the Brotherhood of Steel (BoS) and the Railroad (RR) around, there are several problems with the "endgame" state. Both factions will assume you did their respective quests to completion even if you didn't. People in the RR HQ will talk about Glory as if she is dead even if the battle for Bunker Hill never happened, while the supposedly dead NPC is standing right next to them (although without any dialogue when you talk to her). Even if you never embarked on "Blind Betrayal" and just kept Paladin Danse as a companion, Scribe Haylen at Cambridge Police Station will act as if Danse was exiled from the Brotherhood but you decided to spare his life. Danse might also decide to spawn inside the locked airport warehouse where Liberty Prime is now never going to be built, effectively making Danse unavailable as a companion.