Assassin's Creed 2. At the very last mission where you have to kill the Pope, (yes, THE Pope. Totally awesome, right?), you spend like ten minutes just whacking away at this fat bastard with your sword while four clones of yourself stood around and pretended to be helping, and just as you finally take him down, the game goes "You know what? Fuck you!", and takes control, and pushes you into a cinematic where this 300 pound slob knocks you down, steals your magic... thingy, stabs you in the gut, and runs away as you pass out on the floor!
Of course, you wake up only a few minutes later in perfect health and have to chase down His Holyness and fight him AGAIN. Only now, you have to use your bare hands and beat him into a pulp with your fists.
And then, after all that, once you beat him AGAIN, (Which you will, because he is just as strong as any generic enemy you've fought before, only with about 50 times as much health,) the great and powerful assassin (and don't forget that he IS an assassin) Ezio decides that there has been enough death today or whatever, and decides to let him live.
Just like that, you leave him on the floor, right in front of you, blubbering in the folds of his fat, and walk away. After spending the entire game killing hundreds, if not thousands, of innocent guards and foot soldiers that were only doing their jobs and trying to stop you from killing politicians and nobility, you let the man who wanted TO CONQUER GOD HIMSELF LIVE!
It's a good thing for Ubisoft that they decided to put this crap at the very end, because if this happened during an earlier mission I would have just quit the game right there and then.