“America sleeps in the Divide - giants, beneath the earth. You saw one locked in the silo beneath you. There's more. Only takes a few of them, locked below ground, to tear apart the earth... and cast dust, sand... ash... into the skies above.”— Ulysses
This quest appears after you deal with Ulysses and decide the fate of the nuclear missiles at the temple. Choosing any option other than canceling the launch begins this quest and fails The End. Leaving the temple and watching the DLC ending completes the quest. On returning to the Mojave after the ending slides, a nuclear explosion can be seen in the general vicinity of whichever territory was targeted (or both, if you chose to nuke both Legion and NCR).
The only place where you can find ghoulified Caesar's Legion members is at Dry Wells, if you have directed the nuke to Legion territory (except for the Marked Men).
Nuking a faction will drop your reputation with that faction down to the lowest possible rank (Idolized will become Wild Child, while Liked will become Soft-Hearted Devil). However, it will not turn that faction hostile towards you, even if your reputation drops to a rank (i.e. Soft-Hearted Devil) which would normally trigger hostility. This can lead to the bizarre situation of Legion assassins or NCR hit-squads tracking you into the wastes, running up to you as if to attack, then simply standing around or running away again. However, if they subsequently return, they may turn hostile.
If you complete the quest before confronting Benny, your Legion infamy will be removed once speaking to Vulpes Inculta, meaning you can still secure a positive reputation with the Legion after targeting them.
If you complete the quest before starting the NCR quest Things That Go Boom, your NCR infamy will be removed once speaking to Ambassador Crocker and agreeing to help him. This means you can still secure a positive reputation with the NCR after targeting them.
Both The Apocalypse and The End have the same rewards (apart from the fame/infamy gains). However, with The Apocalypse, the player gains access to the Long 15 and/or Dry Wells, and their subsequent loot. Nuking both yields the most potential rewards.
Everything that ED-E is carrying will be returned to the player's inventory after the quest.