TL;DR: Guys, OT and keep it simple. In any case the People of the commonwealth doesn't build new nuke or thermobaric warheads, they build Dirty bombs / napalm / JunkJets
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Long Version
Uhm... Guys, I think it's a bit out of topic all the discussion about Why/what/when/how can craft nuclear or thermobaric weapons of mass destruction (and by the way: probably the Enclave in Fallout 3 could, it has a supercomputer).
The lore of Fallout isn't one of the most solid on the history of the games (at least, from fallout 3 on).
Fallout 4 moves it to a new level of stupidity that requires a LOT more of imagination
like:
- You don't actually craft a Fusion Reactor, you find one working and move to the base (a dangerous task but, at least, requires only that you know how to shut it down, dismount some easy pieces, move all, rebuild it, then pray that doesn't blow out when turning it on again)
- The Fusion Cores doesn't actually discharge, they are auto-rechargable batteries, so when they end the juice they stop working for, let's say, 2 years and then thery're back at 100% (if not damaged).
- All the tecnology / foods were all standardized to still 'working' in situation of crysis (like a secure plan in case of War, like in the real Cold War)
- And so on...
Just think how many Fusion Cores the BoS will consume EVERY DAY? or How it's possible that a Fusion Core could give energy for 210 years to the remains of a buildings and only for 1 hour on a Atomic Armor? [210 years = 1839600 hours without leap years]
So, please, let's keep this simple or we could discuss about for 5 years.
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Back on the topic:
The ideas about a generic "superweapon plots" is good, but I'd like to call it "Utility Plot" (A way to add those strange bonuses that you get joining a specific faction, like the Vertibird or the Artillery), maybe with a limit of ONE for settlement.
The Orbital Laser still in lore (you can see one in the Broken Steel Dlc of Fallout 3), something like a secondary satellite that you could hijack with specific conditions.
The various ideas about thermobaric, nukes etc. facility -aren't- out of lore, but they're really forced -> If I could build a Nuke, I could probably repair a minor power plant (no flames guys, I mean: it's more easy find an electrician than a team of Nucular physic)
IF I may suggest a different path: The people of the post-apocalypse are simpler: they didn't build an Ak-47, they build Pipe weapons, They don't rebuild a City, they adapt a Stadium.
So they doesn't build a Nuke or thermobaric tactical warheads: they build a 'Dirty Bomb', they build 'Napalm', they build a Shark-a-pult.
[IMO] I think it's best if we remain on THAT line.