I'm a good way through writing my fantasy story, and up until now, my antagonist has been portrayed as being a megalomaniac, and my protagonist (and myself) have believed this to be true.
However, I have had an idea that has suddenly made the antagonist's actions reasonable... while his actions have been more than a bit unethical and high-handed, they're quite justifiable all of a sudden.
The antagonist has been portrayed as a power-hungry megalomaniacal avatar of a god, who has murdered the avatars of his fellow gods in order to weaken them and allow him to gather more worshippers, and he appears to be gathering magical power solely for the sake of the power. The conflict between the antagonist and the protagonist has always been portrayed as the antagonist being the enemy of the protagonist (in trying to kill the avatars of the other gods of the pantheon), but the protagonist being the antagonist's opponent. The protagonist wants the antagonist to resume his natural place in the pantheon, and stop trying to dominate it.
However, the idea that I've had was that the antagonist has been trying to gather sufficient power so that he can go back in time (time travel has already been established being used by the protagonist, and the antagonist should be similarly capable) and enact a change to the world that will lock an even worse antagonist out of this universe forever. In essence, this change has already taken place, so long ago that it is almost forgotten, and no-one knows or really cared how it happened. The antagonist has decided that he must have gone back in time and done the deed, but it would require a stupendous amount of power to pull off... far, far more than he had access to at the time.
My problem is that this provides a good deal of justification for the antagonists's actions, especially considering that if he was actually the one who changed the world to ensure its safety, it could cause a paradox if he failed to go back in time to do the deed. Paradoxes are bad, even - or especially - for the gods and their avatars. It doesn't change the fact that the antagonist has been doing the wrong things... it merely provides justification.
My problem is that I can't decide if this new idea and its implications are a good or a bad thing. Either way, it won't require that I rewrite anything I've written so far... it will just change the nature and the result of the upcoming conflict between the antagonist and the protagonist.
Can anyone say what I should consider in making this decision? Am I making things too complex? Should my antagonist be unexpectedly sympathetic? Have I missed something important in the process of plotting and writing this story?