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The Deepthroat pseudonym is generally associated with Richard Nixon and the Watergate scandal, but as has been well documented, the Metal Gear Solid series draws extensively from real American history to create its world of tactical espionage action. The Deepthroat we see in Metal Gear Solid bears no relation to Mark Felt, the informant in Watergate, but considering the conspiracy themes of the series, it's a suitable reference to make. The name is referenced a few times throughout the series and mostly alludes to Frank Jaeger, also known as Gray Fox.
Even in a series of memorable and larger-than-life characters, Metal Gear Solid's Gray Fox stands out as a fan favorite. A member of FOXHOUND, Jaeger's code name Gray Fox indicates he's achieved the highest rank in the unit. He is a capable fighter whose backstory is integral to the life of Solid Snake. However, Gray Fox only adapts the pseudonym of Deepthroat in the first Metal Gear Solid, but the code name is used throughout the series to reference Jaeger's heavy legacy.
Frank Jaeger
Jaeger appears extensively in the Metal Gear games (as Grey Fox rather than Gray Fox), which were originally released for the MSX2. While they have been ported to a variety of consoles, they never achieved the notoriety that the follow-up Metal Gear Solid series did. Jaeger is initially an ally to Solid Snake, but his loyalty to Big Boss later makes the two enemies. In Metal Gear 2: Solid Snake, Snake must face off against Jaeger before the final confrontation with Big Boss. Snake presumes Jaeger is dead after this encounter, which helps explains why his appearance in Metal Gear Solid is so impactful on Snake.
In the interim between Metal Gear 2 and Metal Gear Solid, Jaeger's body was recovered by the Patriots, fitted with a powered exoskeleton and he was transformed into the Cyborg Ninja. During this time, Jaeger's adoptive sister Naomi Hunter joins FOXHOUND and later works with Solid Snake during the Shadow Moses Incident.
Deepthroat and the Shadow Moses Incident
During the Shadow Moses Incident, Jaeger as Cyborg Ninja infiltrates Shadow Moses island looking for Solid Snake. He has multiple significant appearances as Cyborg Ninja, including removing Revolver Ocelot's hand which then served as a central plot in later games. The code name Deepthroat contacts Snake via codec to anonymously warn Snake of dangers in his path, as Jaeger had done in Metal Gear 2 under the alias of Solid Snake's number one fan.
Jaeger's reveal as Deepthroat comes at the game's climax, as he joins Solid Snake in fighting Metal Gear REX. During this fight, Jaeger also reveals to Snake that he killed Naomi's parents, and asks him to tell her the truth. Jaeger gives an impactful and dramatic speech in which he accepts his death and reminds Snake that while they were both designed to be soldiers, Jaeger found some peace in the end in knowing that he always fought for what he believed in.
Olga Gurlukovich
The impact of Jaeger on Solid Snake is plain to see from the rest of the series, with Snake even quoting Jaeger's final speech in Metal Gear Solid 2. In the same game, Olga Gurlukovich briefly adopts the Deepthroat and the Cyborg Ninja identities which makes Raiden believe that Jaeger may be alive. However, at this point Snake knows the truth of his late friend's fate.
The use of Deepthroat as an alias is certainly a reference to the real-life Mark Felt, as it is just one of many allusions in the Metal Gear Solid series to real-world political organizations and figures. The reference is then given such heavy weight by the nature of Frank Jaeger's character, and his significant impact on both the series and Solid Snake. In fact, Jaeger is the most reoccurring boss in the series, emphasizing his importance to the overarching narrative.