Meanwhile, FBI agents separately learned that two other hijackers also were in the U.S., but headquarters failed to connect the dots and also refused to share the information.
Lawrence Wright picks up the story from there in "The Looming Tower: Al-Qaeda and the Road to 9/11":
O'Neill was a flawed and polarizing figure, but there was no one else in the bureau who was as strong and as concerned, no one else who might have taken the morsels of evidence that the CIA was withholding and marshaled a nationwide dragnet that would have stopped 9/11. The bureau was a timid bureaucracy that abhorred powerful individuals. It was known for its brutal treatment of employees who were ambitious or who fought conventional wisdom. O'Neill was right about the threat of al-Qaeda when few cared to believe it. Perhaps, in the end, his capacity for making enemies sabotaged his career, but those enemies also helped al-Qaeda by destroying the man who might have made a difference.The local bureau quickly determined that Moussaoui was an Islamic radical and believed he might be potential hijacker. It sought permission to examine his laptop, which was denied because the agents could not show a probable cause for their search.
. . . While O'Neill was in Spain, an FBI agent in Phoenix, Kenneth Williams, sent an alarming electronic communication to headquarters, to Alec Station [the CIA's international terrorism center] and to several agents in New York. "The purpose of this communicate is to advise . . . of the possibility of a coordinated effort by Osama bin Laden to send students to the United States to attent civil aviation colleges and universities," the note said. Williams went on to advise headquarters of the need to make a record of all the flight schools in the country, interview the operators, and compile a list of all Arab students who sought visas for flight training.
Jack Cloonan was one of the New York agents to read the memo . . . He wadded it into a ball and threw it against a wall. "Who's going to conduct the thirty thousand interviews?" he asked the supervisor in Phoenix. "When the fuck do we have time for this?"
. . . Then, in mid-August, a flight school in Minnesota contacted the local FBI field office to express concern about a student, Zacarias Moussaoui. He had asked suspicious questions about flight patterns around New York City and whether the doors of a cockpit could be opened during a flight.
When the Minneapolis supervisor pressed the matter with headquarters, he was told he was trying to get people "spun up." The supervisor defiantly responded that he was "trying to keep someone from taking a plane and crashing it into the World Trade Center" -- a weird premonition that suggests how such thoughts were surging through the unconscious of those who were reading the threat reports.O'Neill retired from the FBI on August 22, 2001 and went to work as the World Trade Center's chief of security the next day. He perished on 9/11.
. . . The bureau failed to put together the warning from its own office in Minneapolis with that of Kenneth Williams in Phoenix. Typically it withheld the information from Dick Clarke and the White House, so no one had a complete picture.