Hannibal the Cannibal was a fictitious character.
While irritatedly having a conversation with FBI Special Agent Fox Mulder, Atlantic City Detective Thomas Tomson stated his job, in the city, was to protect people from perpetrators, whether the criminal was Hannibal the Cannibal or Elmer Fudd. (TXF: "The Jersey Devil")
Background Check
"Hannibal the Cannibal" was a veiled reference to Hannibal Lecter, a character who finds a sinister pleasure in feasting on his victims and is consulted by Clarice Starling in The Silence of the Lambs. In the film version of that story, Lecter mentions, "A census taker once tried to test me. I ate his liver with some fava beans and a nice Chianti." The character of Eugene Victor Tooms shares the characteristic of sustaining himself on human livers. In fact, many "Monsters of the Week" that later appeared in The X-Files also had an appetite for human flesh (in "The Jersey Devil" and "Our Town") or specific body parts, such as fatty tissues (in "2Shy") and brains (in "Hungry").
Actor Doug Hutchison, who portrayed Eugene Victor Tooms in first season outings "Squeeze" and "Tooms", took inspiration from the studied stillness of Anthony Hopkins' performance as Hannibal Lecter in The Silence of the Lambs; the stillness of the portrayal had intrigued Hutchison before he played Tooms. (Cinefantastique, Vol. 26/27, No. 6/1, p. 53)
Mulder does a brief impression of Hannibal Lecter in the series finale of The X-Files, Season 9's "The Truth".