If you haven’t found The Nucleus yet, you still have to perform the initiation rites to join the cult of Atom and become a member. Once you’re inside their base, you can perform additional quests for them for some extra equipment and experience or you can proceed with this quest.
Enter The Nucleus Command Center, accessible via the stairwell behind the main shacks inside the submarine base. The prewar security systems and guard bots will be active and will attack you on sight. For more information about the loot that you can get in the area, refer to this guide’s dedicated page for the location.
Continue forth until you reach the end of the tunnel leading to a command center with a security door. Open the door via terminal then don’t examine the console yet. You have to activate the auxiliary power from the fenced off area behind the console. Be warned though, as soon as you activate the aux power, an assaultron dominator will attack you immediately.
When you’re ready, interact with the console and unlock it using Faraday’s program. This sequence will be a bit different from what you normally do so far. There are five puzzles in total and each requires the proper placement of blocks and defenses. Each puzzle sequence is large enough to get its own page so we made a dedicated section in the guide with the solution for each. We also have a basics page if you want to solve the puzzle on your own. You can refer to them here:
After successfully retrieving all memory blocks, you’ll have to do several more tasks like recovering the Wind Farm Kill Switch Code, Uncovering the location of the nuclear launch key, and uncovering DiMA’s secret medical facility. Each of these tasks will open new sidequests.
As a miscellaneous quest, you can also search for the Marine Combat Armor shipments, as marked in the map. Check out this page for the individual locations of the marine armor pieces.
Recover the Wind Farm Kill Switch Code
This is located on a small islet north of Rayburn Point (conveniently marked as "DiMA's Cache"). After recovering it, the quest “Cleansing the Land” will start.
Locate the Nuclear Launch Code
The code is located in Harbor Grand Hotel. As soon as you enter, the quest “Best Left Forgotten” will be completed and this objective willl be added to the “Cleansing the Land” quest. Enter the main hotel building and go to the second floor. You have to go around the broken wall of the kitchen to get to the room with the marked keypad. Interact with it to open a saferoom. There's a holotape on the floor that you can play. There are two ammo boxes in the room, one is novice-locked. There's an Expert wall safe for you to break as well. Once done looting, interact with the terminal and play the security tape.
Now head to the Fringe Cove Docks and follow the quest marker. The nuclear code is found on a sunken boat near the dock, inside a floor safe on the boat's deck. After obtaining the launch key, you'll have new options on how to proceed next. You can use the Launch Key to destroy The Nucleus, confront DiMA about it, or speak to the High Confessor about it.
Uncover DiMA's Secret Medical Facility
You have to visit the Vim! Pop Factory's Factory Area. As soon as you enter the factory, the quest “The Way Life Should Be” will be activated. Head to the mixing vats section of the factory. This is the same area where you can recover the pump regulator for the quest “Ablutions”. In the ground level, there's a security door to the NW corner. Hack the terminal to open the security door then ride the elevator down.
Dig up the unmarked grave then play the holotape. You can also take Avery's locket and skull. Once done, you'll have several options: confront DiMA about Avery's murder, tell Far Harbor about the murder, or optionally, report back to Kasumi about it.