I don't think he plans on killing everybody. He probably wants to destroy the weapons so nobody can use them.
I dought that, especially with the award you get for upgrading divides secret weapon "Rockets’ Red Glare" which is a line in the US national anthem, makes me think that he wants to use whatever is hidden in the divide to recreate America, and sense this is the apocalypse, and sense he hardly strikes me as a pacifist, and sense every fallout game involves someone wanting to wipe the slate clean and start over, it seems unlikely that he has anything in mind save for knocking out both the NCR and the Legion with this weapon.