What about "Knights of the Old Republic"?
When they revealed 3/4 of the way through that YOU WERE REVAN!
That was the "I am your father!" moment that I never saw coming... Brilliant plot twist... within a brilliant game! BLEW MY MIND!
There was also the reboot of "Prince of Persia". Where they reveal the princess' father's role in unleashing the demon... and the way you get involved... EPIC!
One of the best game endings because it wasn't flowers and bunnies, sunsets and trophies... it was dark, human, and seething.