Retcon

Retroactive continuity is 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 Snake's knowledge of his relationship to Big Boss. In a conversation after Ocelot's torture sequence, Snake explicitly state it to Naomi that in Zanzibarland Big Boss told him that he was his "father" before he was killed by him. Such a an exchange does not exist in any version of Metal Gear 2: Solid Snake, Big Boss only mentioning that he and Snake are similar due to their role as soldiers and later yelling Snake's name as he burns.

Before Snake's explanation, Liquid Snake refers to both himself and Snake as "sons of Big Boss." While Snake shows no reaction to this (he presumably assumes that it refers to their place as former FOXHOUND operatives), he later becomes confused by Liquid referring to him as "brother" until Liquid explains that he is also a clone of Big Boss, as well as the genetic process that led to their creation.