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In 2000, after Special Agent John Doggett commented to local Detective Yale Abbott that he himself was somewhat baffled by what he had seen on a case that Detective Abbott was investigating, Special Agent Dana Scully, Doggett's partner, assured the detective that they had seen cases like his regularly on their unit but that Agent Doggett had only just been assigned to the X-files. (TXF: "Patience")
In 2001, following Special Agent Fox Mulder's return and recovery from his abduction, Doggett replied, to Deputy Director Alvin Kersh instructing both Doggett and Assistant Director Walter Skinner to tell Mulder that he was no longer permitted to investigate X-files, by arguing that the X-files was Mulder's unit and that he had created it. (TXF: "Three Words")
Later in 2001, Doggett admitted to Mulder that he understood that Mulder had more than a mere proprietary interest in the X-files but could not help it if Mulder was no longer assigned to that unit. (TXF: "Vienen")
Later that year, Special Agent Dana Scully began teaching a class at the FBI Academy by announcing that, for the past eight years, she had been part of a unit known as the X-files, an announcement that some of her students reacted to with muffled laughter. (TXF: "Dæmonicus")
When Special Agents Doggett and Reyes were questioning Morris Fletcher later in 2002, Fletcher claimed that the reason he had requested to speak with the agents personally was because they now headed the FBI's X-files unit and because he had thought they would appreciate what information he supposedly had to offer them. (TXF: "Jump the Shark")