The Nuclear Option (Minutemen)

The Nuclear Option (Minutemen) is the final Minutemen main quest and an achievement/trophy 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 character 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 they need to traverse.

Opening the map once Sturges finishes his briefing will lead the Sole Survivor to the C.I.T. ruins. However, the true destination is only shown by the compass and will eventually lead 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/Aquagirl perk or mirelurk cake is necessary when opting for power armor.

Once 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 one 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 wading through radioactive water most of the time.

Eventually one will reach an elevated walkway with an 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 one's hacking skills are insufficient to open the door, proceed along the tunnel until reaching another door that is locked with an Advanced-locked door. If the Sole Survivor doesn't have the Locksmith perk, then another door nearby will take them on a circuitous route that will lead to their destination. Make 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 arriving at the room where the Sole Survivor saw the first synths through the damaged wall, continue through another large pipe on the lower level into the Institute proper.

The pipe exits directly into the Relay control room where one needs 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 taking charge of the attack on the reactor. Fight through the Institute forces, turrets and a sentry bot, the latter of which can be destroyed before it powers up if one is quick enough (alternatively, using a nearby terminal will allow it to be powered up before entering its field of view and cause it to become hostile to the synths in the room). After reaching an iris-like hatch on 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 habitat.

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 the Sole Survivor to the Advanced Systems department, only to tell them 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. The player character may speak with him; convincing him to help them by passing an easy charisma check will provide the Sole Survivor with the password for his terminal. The terminal's password is also available on the desk to the left of the computer.

Alternatively, one may simply hack the Novice-locked computer in order to use it to lift the security lockdown. One can also make the rest of the mission easier by shutting down some of the synths (persuade Father for this password), as well as options to fulfill the optional objective by engaging the Evacuation Protocol BD-2, which is necessary for continuing one's work with the Railroad. If the player character doesn't evacuate, the entire Railroad will turn hostile upon meeting them again. Also, Garvey will hate not giving the evacuation order. Once done, head for the Advanced Systems facilities and the reactor.

Securing the reactor involves a firefight in close quarters. The player character will encounter two named legendary synths Z4K-97B and A-2018, which wield heavy weapons and carry the reactor terminal password. The reactor needs to be shut down and the radiation purge initiated before entering safely to place the fusion pulse charge. Talk to Garvey and let Sturges teleport the Sole Survivor to the relay control room where the Sole Survivor encounters S9-23. After the Sole Survivor decides on how to deal with the synth, they must talk to Sturges. This is the last chance to return to collect whatever the Sole Survivor 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 ready, tell Sturges so and step into the Relay. The Sole Survivor will then be teleported to the roof of the Mass Fusion building. Pressing the detonator in front of them will blow up the Institute's reactor and initiate the epilogue cut scene. Talking to Garvey afterward finishes the mission. Should one have made enemies with the Brotherhood of Steel by this point, the next mission With Our Powers Combined will usually start as soon as one gets in Garvey's dialogue range again.

Bugs

 * If the player has completed Underground Undercover, Z1-14 may be in the Relay Control Room and be hostile to the Minutemen when they arrive, but he is essential so he cannot be killed, making it difficult to speak to Preston Garvey.
 * Disabling Z1-14 with console commands fixes this and seems to have no repercussions.
 * When the player teleports to the top of the Mass Fusion building and talks to Preston Garvey the dialogue will never end and keep looping itself, making the quest impossible to finish. If one speaks to him and then fast travels to another location, the quest should complete.
 * Deacon will be stuck in walk mode upon completing this quest with the Minutemen, resulting in him often falling behind when exploring.
 * This can be fixed by typing in the console.
 * One of the Gen 2 synths seen repairing the pipe while moving through the sewer section speaks with a human female voice.
 * If the player is unable to talk to Shaun after the player has planted the nuclear bomb on the reactor, in other words, if the player is unable to proceed to teleport out of the Institute, it can be fixed by using the console commands, or . 1730 will leave Shaun behind and Sturges will confirm this by dialogue. 1720 will take Shaun with the player character, and it changes Sturges's dialogue to fit that choice. If one chooses , Shaun will show up at the Castle and they can get the Wazer Wifle as normal.
 * Upon trying to teleport out, if Mass Fusion was started and the doctor was spoken to, even though it has been failed, the player will get a message "Teleporting to the Mass Fusion building will turn the Brotherhood permanently hostile" though it does not.