One of the most divisive Metal Gear Solid games of all time is 2015's Metal Gear Solid V: The Phantom Pain, which follows the saga of the mercenary group of Diamonds Dogs and their apparent leader and longtime Metal Gear antagonist Big Boss. However, over the course of the game, it's revealed that this purported Big Boss isn't the characters believed him to be all along.
Instead, he's a different mercenary figure named Venom Snake who has undergone facial reconstructive surgery to resemble Big Boss and suffering from longterm memory loss. With The Phantom Pain introducing Venom Snake to the franchise, the game completely changed up the Metal Gear story in its biggest retcon to date, impacting the overarching storyline's history.
Chronologically speaking, the Metal Gear storyline begins in 1964, with 2004's Metal Gear Solid 3: Snake Eater, chronicling Naked Snake during in infiltration mission inside the Soviet Union. Subsequent games following Naked Snake would see the antihero take on the role of Big Boss as he led the paramilitary group Militaires Sans Frontieres (MSF), no longer working with the United States, with he and his army taking on peacekeeping missions around the world.
Set in 1984, The Phantom Pain begins as a story starring Big Boss as the protagonist with his new paramilitary team the Diamond Dogs and the last adventure before longtime protagonist Solid Snake, a clone of Big Boss, is tasked with bringing the rogue paramilitary commander down in 1995 as part of his first mission with the elite squad FOXHOUND in the original Metal Gear game released in 1987.
The Phantom Pain's big plot twist is that Venom Snake was the result of a mission during the events of the 2014 video game Metal Gear Solid V: Ground Zeroes, which was set in 1975. An unnamed combat medic serving under Big Boss is horribly disfigured and rendered comatose for nine years during a mission with the real Big Boss in Cuba.
Awakening in 1984, the medic has no memory of his past life but instead had memories implanted and his physical appearance altered to provide Big Boss with a doppelgänger to take attention away from his activities. By the end of The Phantom Pain, Venom Snake accepts the mantle of Big Boss and takes control of a more proactive, extremist paramilitary group known as Outer Heaven, inspired by a term used by the true Big Boss with the MSF in the 2010 video game Metal Gear Solid: Peace Walker, set in 1974.
This plot twist about the introduction of Venom Snake and his role in taking control of Outer Heaven changes long-held history about the Metal Gear franchise. It was long assumed that Snake killed the true Big Boss in the original Metal Gear game before he mysterious resurfaced years later in Metal Gear Solid 4: Guns of the Patriots, set in the year 2014. This latter iteration was not the gruff antagonist that Solid Snake faced to end the Outer Heaven uprising but someone protective of his genetic progeny. The existence of Venom Snake operating under the guise of Big Boss only helped build Big Boss' reputation, even as it veered more villainous than Big Boss' actual activities.
The revelation of Venom Snake taking over Outer Heaven effectively means that the final boss of the original game wasn't Big Boss but Venom Snake while the true Big Boss continued to operate in the shadows for years. It also accounts for Big Boss appearing alive and well at the end of Guns of the Patriots, treating Solid Snake far differently than his doppelgänger had. While the future of the Metal Gear franchise remains uncertain, despite persistent rumors of a revival, The Phantom Pain twist completely flipped the franchise on its head and proved it still had some surprises up its sleeve.