In Final Fantasy XIV, the Shadowbringers expansion (HUGE SPOILERS AHEAD). Through the vanilla game, and then two expansions, you're either directly or indirectly fighting the Big Bad Guys, whose motivations, history, and abilities are largely unknown to you.

But in Shadowbringers, one of them just kind of... hangs around. Not in the nefarious cloaked form, but as a hyper-powerful sometimes companion that you're not strong enough to fight, and you can use the little help he gives, even if you don't understand his motivation.

Then, over the course of the expansion, you learn more about the guy, learn why he and his group are doing what they do, and as horrible as it seems, it makes perfect sense. And from an objective, 3rd person view, he's right. He even takes you to the Final Day of his world... and the beginning of yours. But even though he's existed for thousands of years and has seen the entire history of your world, he's finally at the point where he can see your side. But he can't stop, because he's fighting to fix his world. And you can't stop, because you have to save yours. And the irony is that both are trying to save the same people, the same world, but either of you winning means the end of one or the other's version of it (think a reverse Tuvix situation).

It was just such a deep feeling to know the other side was right, but still having to fight against them because it would be wrong not to.

Also the music slaps. Especially after summoning 7 other "fragments" of yourself to give Big Man a smackdown.