First go to the game in its dirctroy. Second go to the notepad program named: 
bulidings. Third, there is a long list of bulidings and at the top of the of the
list there is the home base and look for weapon and it says [NONE] change that 
to p-nuke. There. When you play atlantis underwater Tycoon click on the home base
and there is a house with a arrow pointing in to it, click it and you can shoot 
nukes (you can fire bullets from home base but you put in p-bullet, not p-nuke).