XII has war, but the darkness does not stem from that need to survive, and more from man's hubris and how power can corrupt you and fighting for freedom at all costs is not really a good thing, since you can easily lose yourself and others will have to suffer the consequences of your ambition.

I'd say overall VI might be the darkest. Yes, it has tons of mood whiplash, but that only makes it worse. Every time you have a funny or heartwarming scene, you can be sure the next one is going to be of a certain someone nonchalantly decimating a village of innocents or irreversably wrecking the world It's actually that feeling of "death is just around the corner, especially when you least expect it, and all because some people just want more, and you can't really do anything about it" that make it so dark. The world is cruel and unfeeling, and humans are insignificant.