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The agency quickly became top secret and operated out of Area 51 in Nevada in conjunction with the United States Air Force. Their activities included covering up UFO incidents and operating experimental aircraft based on alien technology. They apparently worked with the Department of Defense (TXF: "Dreamland") and the Syndicate. (TXF: "Anasazi") Some members referred to themselves as "men in black." (TXF: "Jump the Shark") They were known to work with the alien colonists. (TLG: "All About Yves")
In 1994, Deep Throat secretly gave FBI Special Agent Fox Mulder an envelope addressed to the commanding officer of the Majestic Project. The details concerned a recent UFO crash in Iraq. (TXF: "E.B.E.")
In 1995, Kenneth Soona, aka "The Thinker," hacked into secret MJ documents and records them on a DAT tape. The documents contained details on everything since the Roswell incident. The Cigarette Smoking Man was sent by the Syndicate to retrieve the MJ documents. (TXF: "Anasazi") Soona was later killed and the tape was returned. (TXF: "The Blessing Way"; "Paper Clip")
In 1998, Majestic stopped FBI Agents Fox Mulder and Dana Scully from entering Area 51. One of the experimental crafts, sabotaged by General Wegman, flew overhead and switched the minds of Mulder and Majestic operative Morris Fletcher and the minds of Hopi woman Lana Chee and the UFO pilot Captain Robert McDonough. After a few days the warp undid itself and time was reversed so that most of the events did not occur. (TXF: "Dreamland"; "Dreamland II")
In 2001, Majestic agent Morris Fletcher allowed himself to be kidnapped by the Lone Gunmen in order to capture Romeo 61 agent Yves Adele Harlow after she stole information on the Maharon project. Majestic captured Harlow and also took the Lone Gunmen into custody for a brief time. (TLG: "All About Yves")