Retcon

Retroactive continuity, or retcon for short, is the alteration of previously established facts in the continuity of a fictional work.

Retcons are present in the Metal Gear series due to the instance of multiple writers, game planning revisions, and prequel creation. This ranges from character backgrounds, plot details, scientific explanations, and much more.

Metal Gear Solid
Possibly the most significant retcon is Solid Snake's knowledge of his relationship to Big Boss. In a conversation after Revolver Ocelot's torture sequence, Snake reveals to Naomi Hunter that Big Boss told him that he was his father sometime prior to his death. Such knowledge is not referenced in Metal Gear or Metal Gear 2: Solid Snake. The lack of concrete evidence, as well as Roy Campbell's response to this revelation, led many fans to assumed that Big Boss told Snake the truth about their relationship in Zanzibar Land, but this is widely considered to be a misinterpretation.

Before Snake's explanation, Liquid Snake refers to both Snake and himself as "sons of Big Boss." While Snake shows no reaction to this, he is later confused by Liquid referring to him as "brother" until Liquid explains that they are both clones of Big Boss, created by the Les Enfants Terribles project.

FOXHOUND operates under the United States Army, instead of NATO.

The Third Zero mentioned in the manual for Metal Gear 2 and to a lesser degree the game itself, involving total disarmament of nuclear weapons, was retconned by the references to nuclear development in various dates that should not have applied to it, as well as the message in the ending. Similarly, Zanzibar Land's nukes were implied to have been developed by Zanzibar Land in the Previous Operations summary for Metal Gear 2 instead of being stolen from nuclear disposal sites, and that the rest of the world had not been aware of Zanzibar Land developing nukes until Dr. Kio Marv was kidnapped.

In addition to the retconning of the Third Zero, the Previous Operations also altered some elements of the story, such as changing the opposing force during the Mercenary War from a joint force of both the East and West to being the CIS, as well as specifying that Gustava Heffner, then known as Natasha Markova, had been a former STB agent. These changes had presumably been done to take into account the fall of the USSR and the Communist Bloc in real life, which had occurred far earlier than projected. Metal Gear 2 referred to the USSR as if it had still existed by 1999 due to the fact that the USSR still existed when the game was first released.

Metal Gear Solid 2: Sons of Liberty
It was stated in the Metal Gear Solid Official Mission Handbook that Donald Anderson was single. However, In the Darkness of Shadow Moses revealed that Anderson had been married to his wife for several years.

Metal Gear Solid 3: Snake Eater
The story established background for the character of Big Boss. In addition, the loss of his eye occurs during the game, which is set in 1964, rather than the 1980s, as previously claimed in the Metal Gear 2 user's manual.

Big Boss's sterility was established to have been caused by the Bravo Shot on the Marshall Islands. Earlier sources, including the Japanese version of Metal Gear Solid, implied that Big Boss had become sterile due to direct combat.

Ocelot's past was established, including his parentage.

Not in Metal Gear Solid 3 itself, but the port for Metal Gear 2 included in Metal Gear Solid 3: Subsistence changed the names of several characters in the game.

FOXHOUND was established to have been founded in 1971, while the Metal Gear 2 manual had earlier implied that it was founded during the 1990s. This retcon apparently had been a last-minute addition, as the leaked MGS3 voice casting sheet mentioned that FOXHOUND was founded in the 1990s. Similarly, Big Boss was also established to have been the founder of the unit, while the same manual simply said he was nominated to be commander of the unit.

Metal Gear Solid: Portable Ops
Frank Jaeger's past was retconned, adding in another confrontation between him and Big Boss in Mozambique, and detailing his involvement in the San Hieronymo Takeover.

Nikolai Stephanovich Sokolov's apparent death during Operation Snake Eater was expunged, having instead survived with the aid a fake death pill from The Boss.

Gene revealed that the CIA had other motives for killing the Boss during Operation Snake Eater, which Big Mama later confirmed in Metal Gear Solid 4: Guns of the Patriots.

Although only in an optional mission, Ivan Raidenovitch Raikov was revealed to have survived Metal Gear Solid 3: Snake Eater. The latter game had earlier left it ambiguous as to whether Raikov was killed or simply knocked out by Naked Snake.

Metal Gear Solid 4: Guns of the Patriots
The founders of the Patriots are revealed to be many of the main characters from Metal Gear Solid 3, including Big Boss.

Implied at the end of Metal Gear Solid 3, Donald Anderson and Sigint are confirmed to be the same person.

Para-Medic is revealed to be Dr. Clark, the person responsible for Gray Fox's augmentation, despite being implied to have been male in Metal Gear Solid. She had also been revealed to have been responsible for the Les Enfants Terribles project, something that had only been implied in an optional radio conversation in Metal Gear Solid 3.

Dr. Drago Pettrovich Mandar survived the events of Metal Gear 2 and is revealed to have been living in Eastern Europe.

Some of Vamp's "superhuman" abilities are explained by the use of advanced technologies, including nanomachines.

Adding to the retcon established in Metal Gear Solid: Portable Ops, EVA confirmed that The Boss had been set up to die by the CIA, as they had feared her charisma.

Not in the game itself, but the supplement Metal Gear Solid 4 Database inferred that Ocelot's affiliation with the SVR and OMOR, mentioned by Naomi in Metal Gear Solid during the boss battle against him, had in fact been falsified to cover up his Patriots-related activities.

Metal Gear Solid: Peace Walker
McDonnell Miller's birth name is revealed as Kazuhira. He was born to a Japanese mother and American father, replacing his previous backstory of being a third-generation Japanese-American, born 60 years after his Japanese grandparents immigrated to America.