Stewart Baker at Volokh Conspiracy has a long post, excerpted from his book, describing some of the background of the "wall", the barrier between criminal investigations and intelligence investigations in the late 1990's up to 9/11.
The right blamed Jamie Gorelick, Reno's deputy AG, but it seems to have been a more bureaucratic story than that. The wall was installed, but was permeable, because FBI agents shared information even though they had different missions (criminal versus intelligence). In other words, their bureaucratic loyalties outweighed paper edicts. But through a sequence of events, Judge Lamberth, Jesse Helms nominee to the appellate court and the head of the FISA court, essentially ended the career of a promising FBI agent who had signed an affidavit, falsely asserting the wall had been observed. That got the attention of the FBI agents. And it meant, as Baker tells it, that the last best chance to uncover the 9/11 plot failed because the agents in position of authority feared for their careers more than they feared the consequences of failure.