X-files was of course, the 1993-2002 TV series (Which had a recent revival in 2016) featuring David Duchovny as Fox Mulder and Gillian Anderson as Dana Scully, FBI agents who were assigned to unusual, usually paranormal cases known as the “X-files”. Fox is partially interested in the paranormal due to the belief that his sister was abducted by aliens, and this is his main driving force in the show. Dana Scully is the more skeptical half, with a side career in medical studies which comes in handy on many of their cases.
In their cases, they also begin to unravel a complex-and often contradictory-conspiracy dealing with an attempt at an alien invasion, aided by the mysterious group known as the Syndicate, with their primary representative being the Cigarette Smoking Man, who has influence in the FBI, and especially has an interest in Mulder. The syndicate hopes that when the aliens invade, they will be spared.
And yes, Solid Snake smokes too. But that’s far from the whole similarity.
Both Metal Gear and X-files have two informants that are in a way, both friend and foe-and both go by the code names Deepthroat and Mr. X. In X-files case, these are syndicate members who have decided to either aid or misleed Mulder.
In Metal Gear’s case, “Deepthroat” is in fact the Cyborg Ninja version of Grey Fox, who helps Snake past some tricky spots so they can do battle again. (In Metal Gear II, Solid Snake had fought Grey Fox-one of the captives in the first game who switched loyalties to Big Boss in the second-and left him for dead).
Mr. X’s story is a bit more complicated. Mr. X is in the intact Olga Gurlokovich, who is working with Solid Snake in secret to get revenge on Revolver Ocelot for the death of her father, and also because her daughter is being help captive by agents of the Patriots, so she’s forced to work for them as well, taking on the ‘role’ of the Ninja in the Patriot’s scenario-the Big Shell Inciddent-which they’re trying to use as test data.
As for the Patriots themselves, they start off as a group of humans, not unlike the Syndicate. Not just any humans, but those who had survived the Snake Eater mission-Big Boss, Eva, Para-Medic, Signit, Ocelot, and the mission commander Major Zero. Their initial goal is to unify the world and realize the dream of their fallen friend The Boss, but unfortunately Zero and Big Boss clash on the way to do it, leading to a total fallout between the two, with Big Boss forming Outer Heaven and Zero, with the loyal members, creating the Patriots AI and the Les Enfant Terribles-Solid Snake, Liquid Snake, and Solidus Snake-something which drives the plot for the rest of the series.
Apart from that, there’s a few other things which are paranormal about Metal Gear-The Cobra Unit (The Boss’s world war II unit) has many paranormal attributes-one’s semi-immortal, and one’s even a ghost! Plus there’s a guy who can control bees, and another who walks like a Spider.
In Peace Walker, Amanda’s younger brother Chico has an obsession with paranormal phenomenon, in particular UFOs and unidentified mysterious animals, or UMAs. This actually was done in part as a (non-canon) crossover with Capcom’s Monster Hunter series, with a few optional missions dedicated to Big Boss fighting monsters, including one that resembles Metal Gear REX.
In addition, when Chicho tries to sell a photo of the Chrysalis AI weapon to a magazine, he sets off an inquiry into UFOS.