fascistcrusader
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Three atomic bombs isn't very impressive even by todays standards. An atomic bomb is a fission powered weapon, much weaker than today's thermonuclear fusion based weapons. Three A bombs would only destroy outright an are with a diameter of about 2.25 miles. Even with 50 ships it would take hours to glass a planets surface using this weapon.
Even with this, like most Sci Fi weapons the energy is probably concentrated and doesn't spread out like a nuclear explosion. The turbolasers of Star Wars, for example, have energy outputs in gigatons according to official materials. This is far greater than the most powerful thermonuclear weapons of today, but they only affect a very small area because the energy is packed into one location.
Then even after this, Kuja's durability is ridiculously high, he tanked a nuke like barrage from Bahamut with nothing but a scratch on his forehead, and in Trance he's even more powerful. My money says he'd laugh off hits from these weapons while Ultima-ing them into oblivion
Then they'd have to deal with God Kefka, a being with all of the magic in his world with enough power to do things like rearrange the continents on a whim or nuke cities from across the globe simply because they didn't like him. He would lay waste to any ship thrown his way.
Then there's AC Sephiroth, who could just teleport into or phase through the walls of any ship and cut down everyone inside unopposed. Heck, he might be able to just cut the ships in half.
Then to add to this unholy trifecta, you've got summoned beasts to deal with, creatures like the Cloud of Darkness that can destroy all life in the world, and things like Sin, which is basically a whole fleet's worth of firepower in on monster.