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 which 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 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 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 in 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 lock down. 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 opt 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 fire fight in close quarters. The player character will encounter two named legendary synths Z4K-97B and A-2018, that 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 afterwards 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.

Keeping all three factions alive
The fastest way is to simply become banished from the Institute upon arrival at the Institute, but to get the most out of all main faction questlines while finishing the game for the Minutemen, do the following:


 * 1) Join the Minutemen by saving them in Concord and helping them rebuild Sanctuary Hills, retake the Castle including its Old Guns and set up a total of at least eight settlements throughout the Commonwealth.
 * 2) Continue the main quest up to Institutionalized. Be careful not to alienate Father by acting consistently hostile towards him during the first meeting or he will ask the Sole Survivor to leave.
 * 3) Give the holotape from Inside Job to Sturges first. This is only available if the signal interceptor is built with the Minutemen in The Molecular Level.
 * 4) If the Railroad has not been destroyed, assist them until asked to "continue working with Father" during Underground Undercover. Keep in mind that this quest will fail if the Brotherhood of Steel is left alive.
 * 5) Help the Brotherhood of Steel up to the quest Blind Betrayal. Receive and complete the quests Duty or Dishonor and A Loose End for Lancer-Captain Kells before finishing Blind Betrayal, or the player character might miss out on two of the very rare unique power armor pieces.
 * Alternatively, one can complete Blind Betrayal (and optionally get Danse's perk afterward). In that case, Tactical Thinking will start when Maxson orders the Sole Survivor to speak to Kells. Avoid Kells until after the Institute is destroyed, speaking to him will make the Sole Survivor an enemy of the Railroad.


 * 1) Do any and all quests for the Institute up to Mass Fusion.
 * Do something to get banished from the Institute, such as killing a named scientist or Father. Or accept Mass Fusion, but instead report it to the Brotherhood, which will immediately start Spoils of War. Complete Spoils of War for the Brotherhood and this will automatically fail both the Institute and some of the Railroad questlines and allow the Minutemen to be led to victory while still having the Brotherhood of Steel around, resulting in three of four main factions surviving the end game (although one still has to be careful to keep this peace while pursuing more of their respective quests).
 * If the signal interceptor was built by the Brotherhood instead of the Minutemen, Inside Job will immediately start when banished. The quest log will require one to retrieve the Network scanner holotape from Proctor Ingram aboard the Prydwen, or Boston Airport if From Within has been completed.


 * Do not proceed through Brotherhood quest straight away after gaining access to the Institute, except for From Within and Duty or Dishonor. Instead, follow the Institute questline until reaching Mass Fusion, since this is the only way to get Spoils of War without starting Tactical Thinking. Also, do not hand in Blind Betrayal to Maxson before finishing off the side quests from Kells (The Lost Patrol, Duty or Dishonor and A Loose End), since talking to Kells afterwards will proceed Tactical Thinking to the point one is hostile to the Railroad.
 * If one chose to complete Blind Betrayal (above), then Underground Undercover will fail. Report the player character's banishment to Desdemona instead of the Brotherhood. She will direct them to Preston Garvey. In this case, both Mass Fusion and Tactical Thinking will also fail. The player character will never get Spoils of War therefore never getting a main quest mission to the Mass Fusion building. One can, of course, go into the Mass Fusion building at anytime to acquire the Strength bobblehead.
 * It is possible to speak to Proctor Ingram by moving the mouse to the right side of her, avoiding a conversation with Kells. Using Console Commands to set Tactical Thinking to complete, and to instigate Spoils of War, makes completion of Spoils of War, completion of Blind Betrayal, and a three-faction peace still possible. It is still possible to complete Blind Betrayal immediately after having completed Spoils of War.


 * If one does not issue the evacuation order before leaving, the Railroad including Deacon will become hostile the next time the player character speaks to Desdemona.
 * Depending on how the player character completed quests prior to this, this is the best ending possible, in which both the Brotherhood and the Railroad can survive. This outcome may be completely unintentional, as characters in either faction will speak and act as if only they and the Minutemen survived; for example, P.A.M. will still offer A Clean Equation or High Ground quests, as if the player character had previously destroyed the Prydwen and sided against the Brotherhood.

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-travel 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 teleporting 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.
 * Upon using the central elevator after Sturges directs you to open advanced systems, the elevator may descend and then re-ascend to the top floor. From this point, when the player tries to access the elevator, a notification will pop up saying "Elevator access denied". The elevator will be inaccessible.