The setting of Fallout is mature and dark. A post-apocalyptic wasteland where mutants, cannibals and horrible monsters freely roam. In a setting so complex and desperate, humanity is on the edge of morality. Several quests can be concluded in a really evil way, especially since the game allows complete freedom also in who to kill. Of course, in a nuclear wasteland, radiation and nuclear power are a big part of the moral equation. Few but memorable quests exploited the power of the atom, with a brutal and devastating result. Of course there will be light SPOILERS on some quests in Fallout 3 and New Vegas.
In Fallout 3, the wrong use of an unexploded atomic bomb will have a catastrophic result, which was never achieved again in videogame history. Megaton is a town build around an old atomic bomb. People almost worship the bomb, considering part of the town and of the religion. The huge bomb can easily be disarmed, putting the town in safe. But a rich and powerful man has a different idea: to trig the bomb causing the annihilation of Megaton. After triggering the bomb, the player should travel to the tower were the rich man is living. There, the player will discover the truth behind this evil quest. A simple and so disturbing truth.
The horrible shape of Megaton is ruining the view from the balcony of the man. For this simple reason, he wants the town completely obliterated.
The player can now press the apocalyptic switch, causing one of the most massive nuclear explosion in a videogame. A beautiful but tragic bomb of light that will end the history of Megaton. The town will disappear from the map, leaving behind only a highly-radioactive dump. All the people living there, the shops, the quests and the items, are now gone forever. Few key characters will survive, but horribly mutated in ghouls. Destroying Megaton is considered the most evil act in Fallout 3, causing a massive drop in the Karma moral system of the game.
This is why the quest is called “The Atomic Power”.
In the sequel, Fallout New Vegas, during the main game the player cannot play with moral and atomic power. However, the situation drastically changes during the DLC Lonesome Road. At the very end of the main quest of the DLC, the player will have access to a nuclear silo, with two warheads still operative. The good way to conclude the quest is to stop the launch by disarming the weapons. But of course, there is another evil way of ending the quest, which is called “The Apocalypse”.
New Vegas is a game focused on siding with different factions, working on increasing the reputation with them. The two biggest factions are NCR and Legion, which of course are enemies between each other. Controlling the power of nuclear weapons, the player has in the hands the instrument to decide the fate of the world. Depending of which faction the player joined, he could decide to use the missiles on the other faction. This evil act will cause a massive drop in the reputation with that faction, very understandable since the player almost annihilate them.
If this choice is evil but quiet influenced by the system of factions in the game, the next hidden choices is plainly evil and anarchic. Since there are 2 nuclear weapons, both the factions can be destroyed at the same time. A very weird choice, but still possible. The nuclear explosions also in this case will change the environment, creating radioactive wastelands full of mutants, where before there were the headquarters of the two factions.
In Fallout 4 DLC Far Harbor, the headquarter of a faction which reside inside a submarine can also be annihilated by launching one of its warhead on itself. This will cause a massive nuclear explosion that will completely destroy the submarine and the faction.
Apparently, even in the online-only Fallout 76, the players can access codes to launch nuclear weapons from specific silos to the CAMP of other players.
I don’t know if other chapters in the Fallout saga allowed the player to morally play with the nuclear power, but these ones are for sure the most massive and amoral ways to use atomic weapons. Not only this will kill dozen of characters, but will also change the environment and the world permanently.