In his new book Intelligence Matters, retiring Florida Democratic senator Bob Graham, former chair of the Senate Intelligence Committee, tells how his staff discovered that one of the FBI's own informants knew two of the hijackers and rented a room in his house to one of them. Congressional investigators wanted to talk to the informant and tried to have the FBI serve him with a subpoena. But the FBI refused to cooperate, and actually took steps to obstruct Congress from getting to the informant by hiding him in a new location "for his own safety."
Meanwhile the press had revealed the man's name. At that point, this informant with little money of his own suddenly was being represented by an expensive lawyer with close ties to the FBI. And to the end of this episode, the FBI refused to cooperate, insisting that references to this informant be removed from the committee's final unclassified report and rejecting any idea of public hearings on the subject.
Maybe the FBI was just embarrassed, or as Graham writes, "A far more damning possibility is that perhaps the informant did know something about the plot that would be even more damaging were it revealed, and that this is what the FBI is trying to conceal."
Additional reporting: Laurie Anne Agnese and David Botti