The Nucleus

This is the base of operations of the Children of Atom cult which is a former submarine base. This location is where DiMA once stayed. He is friends with the late High Confessor, Martin, and he gave the base to the Children as an act of friendship and goodwill. In addition, the pre-war computers in the base is where DiMA offloaded some of his previous "memories" due to his hardware limitations.

The first time you visit, you'll find Richter executing two members due to an “issue of loyalty”. Talk to him and if you showed interest in joining the cult, the quest "Visions in the Fog" will start. Even if you're not yet a member, you can loot some of the items found in the outer portion in the Nucleus. There's an explosives crate in the upper ledges.

After doing the initiation quest and gaining access to the interior of the base itself, head to the decontamination arc and pick up the note near the button. The arc isn't functioning and picking up the note will add a new objective to the “What Atom Requires” checklist quest.

You can also pick up two fusion cores on a shelf inside the shack beside the submarine.

Talk to Zealot Ware (one of the bald guy with armor and weapon) and he'll talk about convincing Brother Devin to quit his fasting. If you agree to talk him out of it, the quest “The Trial of Brother Devin” will start.

In the upper shack in the middle south (local map), you'll find The Archemist. There's a chemistry station you can use here and an unlocked safe. She is the Nucleus' doctor and you can avail medical services from her.

Kane sells weapons, including a couple of unique items like Kiloton Radium Rifle and Recon Marine Left Arm. He strictly sells during the specific time of the day his shop is open. Unlike other shopkeepers, he'll refuse selling you anything if you wake him up from his sleep.

Talk to Sister Mai and ask her if she needs help with anything. She'll mention about recovering a pump regulator from the Vim Pop factory. If you agree to recover it for her, the sidequest “Ablutions” will start (Longfellow will dislike this decision) There's another unlocked safe under her table as well. Behind her shop is an armor workbench.

In the floor above, there's a weapon workbench, power armor station, some lootable containers, and another unlocked safe under the table. Talk to Richter to start the quest The Heretic.

Nucleus Command Center

In the highest point of the base, there's a door leading to the Nucleus Command Center. This leads to the base's Command Center but you'll only be able to access the security door containing the valuable computers inside during the story quest "Best Left Forgotten". However, you can still get rid of the security emplacements and robot guards early even if you don't have that quest yet.

If you open the door the right, it will lead to a deadend room with weapons workbench. In the main path, you can go past the security systems by either destroying the turrets or disarming the tripwires.

Continue forth and you'll encounter another MG turret on the wall before the first corner. In the next room, there's a hostile Colonel Gutsy. There are also two sleeping quarters with lootable containers nearby. Proceed then destroy the two Protectron Watchers in the mess hall.

Continue following the path and loot any containers you encounter along the way. You'll eventually reach another room with an assaultron and protectron watcher. Destroy them then loot the green steamer trunk near the terminal. You won't be able to access the terminal for now since it requires a key so take the other door instead. This will lead you back to the Nucleus.

You can check out one of the open rooms there to find some duct tapes and tons of aluminum and tin cans. Check the other remaining open rooms to find more components for crafting.