RpNation

Do the responsible thing to take care of your villain; have them become blinded by lust for power, obtain said power, and transform to a state in which they have a weakness they're unaware of such that their opposition can pull a fast one on her.

Or do the better thing and have them ascend to Goddess status so they can take over their respective universe and/or dimension.

Put a Bullet in their head, then there is the make an even stronger good guy route who kills hinself along with the villain, also the spontaneous death is another