Massive SPOILERS for the twists of the games follow.
In Metal Gear, there’s a great deal of duality in the characters-some characters assume dual identities, and some even believe they actually are different people. While some of this can be chalked up to the characters having nicknames or code names-such as many of the Snakes-there’s other things at play as well.
The first, and most important in MSX’s first Metal Gear game, is Big Boss himself, who is initially Solid Snake’s Foxhound commander, but is also secretly developing his mercenary state Outer Heaven and Metal Gear TX-55, and he fully intends Solid Snake to fail the mission. The Outer Heaven commander is initially unknown, but is revealed to be Big Boss at the end of the game.
This in turn prompts another twist (or a bit of retroactive continuity) in the latest Metal Gear Game, Metal Gear Solid V The Phantom Pain. It’s revealed that the Big Boss Solid Snake kills at the end of the game is, not in fact, the real Big Boss, but a medic from Big Boss’s 1970’s mercenary force Militaries San Frontieras, who was hypnotized/brainwashed and physically altered into believing he was the real Big Boss after a helicopter crash that resulted in both being in a coma for nine years, although he’s able to largely shape his own legacy, working closely with Miller and Ocelot, and developing the mercenary group Diamond Dogs (While also stopping a parasitic outbreak and defeating another Metal Gear) while the real Big Boss works building FOXHOUND.
This “Phantom”-AKA Venom Snake-worked with the real Big Boss, and once the Phantom is killed, Big Boss is forced to leave Foxhound as his cover is blown, and then starts up another nation-Zanzibar land-later on.
In addition-Schneider-a character in the first game-resurfaces as a ninja. This will become a running theme in the series.
The original Metal Gear Solid likewise has quite a few twists. After botching an attempt to interrogate DARPA Chief Donald Anderson, and hence not being able to get the launch codes for Metal Gear, Liquid Snake and his ROGUE foxhound group construct a plan to give Snake misleading information so that he’ll actually practically give them the codes on a silver platter.
The first is by having one of his soldiers, Decoy Octopus-a master of disguise impersonate Donald. This goes somewhat awry as Octopus succumbs to the FOXDIE virus implanted in Snake, though.
It is also eventually revealed that Big Boss’s technical consultant during Operation Snake Eater-SIGINIT-and Donald Anderson are one and the same.
The next step has Liquid Snake impersonate Snake’s mentor Master Miller (Who has been murdered) over the Codec Radio. In addition to tricking Snake into giving him the codes and card keys, Liquid also spreads distrust among Snake’s support team, especially against Campbell and Naomi Hunter.
The biggest twist of all though is that the whole incident was in part, set up by Liquid’s second-in-command Revolver Ocelot (and the only survivor of the rogue Foxhound group), who was secretly working for Snake’s other brother, Solidus.
Likewise, a ninja with questionable loyalties assists Snake on the mission, just like Schneider before. In this case, the soldier is Gray Fox, a former FOXHOUND operative who Snake rescued-and later fought-in the last two games, but twisted into a cyborg by The Patriots.
Likewise, after events go awry on a tanker in New York in Metal Gear Solid II, Snake is forced to go into hiding, and adopts the name Iriqous Pliskin as a cover. Likewise, Solidus chooses his brother’s code name when he takes over the Big Shell cleanup facility as leader of the group “Dead Cell”.
Before the game is over, “Iroquois”‘s true identity is revealed, and he once again becomes Solid Snake.
Likewise, there’s another cyborg ninja,who turns out to be Russian double agent Olga Grulokovich (although she is not physically damaged like Grey Fox)
There’s also the computer AI who impersonates Snake’s former superior Colonel Campbell, something made abundantly clear when a computer virus causes it to malfunction:
Raiden, the game’s main playable character, is also somewhat of a duality. He goes by the codename of “Snake” initially, although it’s later switched to “Raiden”. Turns out many of his memories-including being a child soldier working for Solidus-have been repressed as well.
Raiden later becomes yet another Cyborg Ninja, although one with a far better fate than most of his predecessors.
But perhaps the most famous of these phantoms is Ocelot himself. In addition to his double agent status at the end of Metal Gear Solid, he’s been secretly working for Big Boss and Eva pretty much all along, and trying to overthrow the Patriots AI (and working both sides during the “Snake Eater” conflict), he creates a complex plan, one that involves attaching Liquid’s arm to his own missing arm, and using hypnotism on himself to make himself think that he is possessed by Liquid’s spirit somehow (similar to the technique used on the helicopter medic to fool him into thinking he was Big Boss), fooling the Patriots. This sort of creates a new combined version of Ocelot and Liquid, “Liquid Ocelot”. This deception ultimately pays off, allowing Snake to defeat the Patriots AI (Although Ocelot perhaps wanted the world to descend into anarchy, in a sort of twisted reflection of his idol Big Boss’s dream.)
In the PSP prequel Peace Walker, we have Paz Ortega. Initially believed to a pacifist student at a local university in Costa Rica, she is in fact an agent of the Patriots (Then largely called Cipher). This is revealed at the end of the game, where she controls Metal Gear ZEKE and reveals her real name, Pacifica Ocean.
Although she survives Metal Gear ZEKE being damaged, she’s then taken and interrogated by Skull Face, and further booby-trapped, creating the explosion that puts Big Boss and the later Venom Snake into a coma. However, Venom Snake’s trauma and overwhelming guilt over the incident causes him to hallucinate a scenario where she survived, although this “reality” soon unravels too.
There’s also an AI POD in Peace Walker, which has been programmed to replicate the mind of Big Boss’s mentor/mother figure, the Boss, and used to control the Peace Walker weapon. This eventually allows him to the defeat the Peace Walker, as the AI Pod rebels and submerges the semi-Metal Gear.
Believing the action to be the Boss’s will , Snake-believing that she put down her gun and betrayed their soldier’s ways-finally accepts the title of Big Boss, becoming more of the villain of the original games.
The AI pod also resurfaces (literally) in the Phantom Pain, and used in part to develop the Metal Gear Shelanthropus. It also-unfortunately-serves as a grim coffin for the scientist Strangelove, who is betrayed by her husband Huey Emmerich and sealed within.