Since I haven't seen it mentioned yet, Darkness II.
I saw that twist coming from the beginning of the game, but I still enjoyed it.
Bastion
Grandia II
Prey
Mass Effect Trilogy
Knights of The Old Republic
I actually had that one spoiled for me, but it is still a very memorable twist.
Final Fantasy VI
It turns out the visions Jackie was having about his dead girlfriend wasn't the Darkness messing with his head, but the Angelus who had taken Jenny as its new host.
Bastion
The Bastion as actually a machine that has the power to reset reality, perpetuating an endless cycle of destruction and rebirth with nobody being any the wiser.
Grandia II
Granas(God) is actually dead, having been killed in his battle with Valmar(The Devil). Then it is revealed that Pope Zera is actually the main villain, and is attempting to take Valmar's power for himself.
Prey
The Keepers turn Tommy's girlfriend--who he had been spending the entire game trying to save until that point--into an abomination... and Tommy is forced to euthanize her himself. Then it is later revealed that the entity that has spent the entire game chiding Tommy was a Human once.
Mass Effect Trilogy
Sovereign is actually a Reaper... and the Mass Relays and Citadel are actually a Reaper trap designed to keep Galactic civilization from getting too advanced.
The revelation about the Keepers.
The Collectors were once Protheans.
The Protheans were actually a very brutal empire who forced lesser races into subjugation, instead of the benevolent Paragons of society that we had been lead to believe until that point.
EDI was the Rogue VI that Shepard "killed" on Luna in the first game.
The revelation about the Keepers.
The Collectors were once Protheans.
The Protheans were actually a very brutal empire who forced lesser races into subjugation, instead of the benevolent Paragons of society that we had been lead to believe until that point.
EDI was the Rogue VI that Shepard "killed" on Luna in the first game.
You are Darth Revan.
Final Fantasy VI
Kefka betrays and murders the emperor, destroys the world and literally becomes a god in the process.