Close second: StarCraft 2.
Starcraft 2 is some impressive fuckery. The millenia-old hive mind of the not-tyrannids wasn't a bad dude really, just under the influence of some fucker named Amon. Oh and the hive mind still managed to infest this one gal, Kerrigan, because it knew she'd be prophesized to be the only One capable of killing the big bad.
This then, hilariously, leads to: Kerrigan, mass-genocidal murderer, isn't a bad dudette really. Just under the influence of some fucker named Amon. Oh and Jimmy still loves her despite not Knowing this, making Him save her, even though he swore he'd be the man to kill her.
Also giant naked angel of fire ending with so much space magic it'd make Ron Moore blush.
Starcraft 2 is a fantastic game, with this one glaring exception. I don't mind a stupid space magic extravaganza, it's just tonally a real effing weird swerve to make in the sequel to a fairly shades of grey dirty space warfare game.