Ending 1:
A goddess is revealed to be the final enemy. I won't bother you with the why and how, but the bullshit part of the end is basically that she just snaps her finger, Naofumi and his party gets wiped out in battle with her after not being able to inflict any damage. The skill she hits him with first is 100% hit, 100% death and the speed "exceeds infinity".... yeah, but somehow he blocks that. Then she kills him by erasing him from this world and all other realities that exist... err, ok? So he, together with the other heroes, dies. He then reawakens in his original world in the library where he opened the book that got him into the other world, and Raphtalia is with him. The end.
So the readers were pissed with this ending to no end, because it just came outta nowhere and left the entire story totally unresolved. It felt like it had gotten the axe, but really that was the ending the author had in mind. Just imagine a road trip movie that is just somehwere in the middle of the arc and suddenly outta nowhere the car crashes into a wall and the credits roll.
So after getting buttloads of flak, a few extra chapters were added.
Ending 2:
Naofumi and Raphtalia manage to return to the world after basically ascending to godhood themselves. Combat between gods now happens via "concepts". Which is really nothing more than childish bullshit from the sandlot along the lines of "my shield blocks infinite amount of damage" - "yeah, but my attack does infinite damage +5!" - "then my shield now blocks infinity x5 damage!". Yeah, that kind of idiocy. They beat the goddess, save the world, and Naofumi, Raphtalia, Firo and Atlas become eternal guardian gods over the world.
It's a better ending as in that it actually resolves things instead of just suddenly being over. But the entire story of how they ascend to godhood and the battle between gods itself is a total clusterfuck and cringeworthy without end. It really feels more like pre-schoolers bickering instead of an epic fight between gods.