You're definitely trying to prevent an evil alchemist from remaking the world as a god in Atelier Iris: Eternal Mana, but that's the only one I've played so I'm not the most qualified commenter in that regard.
In Disgaea: Hour of Darkness, Laharl starts out trying to become Overlord in the first half of the game. In the second half he fends off invading humans, then either A) attacks the Angels' world of Celestia to find out why they put the humans up to attacking the Netherworld or B) conquers Earth. Laharl's not really saving anything, just asserting dominance. Disgaea 3's characters are also more concerned with glory, revenge, or self-preservation than with saving anything. Disgaea 2 and 4 definitely end up being about world-saving, even if they don't necessarily start that way.
My favorite indie RPG, Cthulhu Saves the World, is less about saving the world and more about Cthulhu trying to regain his powers by righting wrongs out of frustration. I'm not even sure if the world was in any danger when you defeat Azathoth at the game's end.
Oh, and I'm also not sure about Shin Megami Tensei: If... (which I admittedly have started, but am not even close to finishing). I think you're only trying to save your school, not the world.