ITT: we talk about times a video game actually did something you didn't expect.

White Knight Chronicles did this for me. Playing it, it was "generic western story, with Japanese flavor added". 90% of the game was "your princess is in another castle". Then you reach the end of the game.
Literally all the rules you THOUGHT existed are broken in a matter of a single event scene, while remaining completely logical. [SPOILERS]The princess gets shanked, your ally gets killed, and fused with one of the major villains, turning into[/SPOILERS] the final boss, who, while you have the ability to transform into a giant robot, is the size of a giant robot your giant robot could have transformed into. A giantER knight. Cue epic chanting and final boss music "The Devil on a Black Horse". It was one of the only final bosses in a video game that I spent over an hour fighting, had to level up at least 5 levels for, and still lost - so it was difficult to say the least.
tl;dr
The game went from "I can literally say what's going to happen next" to "Holy shit, this is fucking crazy!".