I'm gonna go with Suikoden II.
The story is dark and troubling, partially because it has one of the best villains ever in Luca Blight, but mostly because it takes two best friends and throws them at one another. When their village is invaded and burned to the ground, the two friends are separated. They each end up in separate places and they each rise to power in different ways. The war and the tragedy has changed them both and made them into enemies with different perspectives and philosophies. They cannot go back but going forward means going through the other.
Damn it, that was a great game.