2. Metal Gear Solid 3: Snake Eater
In particular Metal Gear fashion, a search for a nuclear weapon soon becomes a mission involving extraordinary people with extraordinary powers trying to kill you, before ending in a man versus giant machine climax. But Snake Eater, arguably the best installment, went one step further with an added emotional betrayal that wasn't what it seemed. And only became clear after it was too late. Playing as Big Boss aka Naked Snake, having defeated the Shagohod your final mission is to kill your lover and mentor The Boss for having defected to the Soviets and starting this whole mess. But once you've killed her she tells Snake that she was in fact a double agent, and had been helping him all along in his mission, and that she knew this would be how it would end when she accepted the mission. She goes down in history as a traitor, and Snake succeeds her position but isn't happy about it at all. For his country he betrayed everything he'd believed in. In the final scene, he lays a rose at her grave and sheds a tear as he salutes her. It's an emotional end in a game you'd least expect it.