Neon Genesis Evangelion, Vol. 7

On the surface, this seemed like it was going to be a fairly standard adventure hero sort of plot. His friends dead and injured, our protagonist leaves the Evangelion project, returning only after the city is attacked again and he realizes that he alone can save it.

Of course, this being Evangelion, there is a lot more than just that going on. We learn the real reason that all these monsters keep attacking Tokyo, and the relationship that the NERV organization has with the tragedies that have killed half of Earth's population. Most shockingly, we also learn that the giant robots aren't actually giant robots, but living things, and we see our hero get broken down on a quantum level until only his disembodied spirit exists within the hulking frame that he used to pilot.