The Men in Black are said to be employees of the CIA, who badger and threaten extra-terrestrial encounter witnesses to keep them from spreading details of the event.
The Central Intelligence Agency (CIA) is a Government organization dedicated to protecting America. They are one of the highest powers in the United States, and for this reason, some believe corruption and misappropriation may be rife within the organization.
In San Andreas, a division of what is thought to be the CIA makes a brief appearance and attempts to kill CJ during several missions for Mike Toreno. They can be seen using a unique M4 assault rifle during the mission Stowaway.
Although in real life, the Men In Black are said to deal with extra-terrestrial encounter witnesses, in-game, they seem to be simply a part of a corrupt division of the CIA, although the agency is never named. There are only 2 agent skins in game, one black and one white, which is thought to be a reference to the film, Men In Black, starring Tommy Lee Jones and Will Smith as the protagonists.
In San Andreas, Men In Black is a fan-coined term, so it is likely players had this movie reference in mind, when they first discovered this myth. The agents also mutter strange references to UFOs and extra-terrestrials, while on-board the Andromada plane, another likely factor.
GTA V Reference
In Grand Theft Auto V, the theme of the mission Minor Turbulence seems to be quite similar to Stowaway and may be a reference to the popular San Andreas mission, although, Merry-weather Mercenaries take the place of suspected CIA agents in the installment.
It is unknown exactly what the Men In Black are up to during the mission Stowaway. Their mentioning of Aliens and UFOs aboard the Andromada are one of the many references to extra-terrestrial activity in the game, particularly during the Desert missions.