Spoilers, obviously. I tried to include one per game otherwise it'd be a wankfest for Planescape: Torment.

-Final Fantasy VII: Cloud's memories are just a clustersmurf of trauma and insecurity.

(SPOILER)-Life is Strange: Chloe's death must be rewritten for Arcadia Bay to survive. Not really a twist but it was very thematically fulfilling.

-Silent Hill 2: James killed his wife.

-Planescape: Torment: Dak'kon was introduced to the teachings of Zerthimon by The Nameless One and was forced into an eternal slavery by him.

-Final Fantasy VI: Kefka causes the apocalypse.

-Tales of the Abyss: Luke is Asche's clone.

-Fallout: New Vegas: Mr House has been cryogenic ally frozen as to preserve his empire

(SPOILER)-Undertale: No one has to die.

-Chrono Trigger: Chrono dies.

-Baldur's Gate: You are the child of the God of Murder and Sarevok is your brother.