Something that I liked in an old game from...I think PS2 days. Vagrant Story.
It's a huge spoiler for...well the entire plot of the game, so I'll blur it.
The fact that the badguy at the end, is actually not a "Bad Guy", but is basically the vessel for a very dark power, and he's trying to get rid of it, as he's grown weary of wielding it. So the entire game, his cliche supervillain "Join me! and you will know power unimaginable!!" was a ruse, a test, because he didn't want to give it to someone who would be a monster with it. So the fact that you were constantly defying him, resisting his temptations, and staying virtuous, made you the PERFECT person he was looking for. So in the end, you defeat him, and take on the mantle of the dark power, confident that you will show restraint in using it. It's very much like that Heath Ledger film The Order, as far as motivation of the antagonist.
I just really enjoyed it.