Continuing to keep information from the FBI, Schmidt is fired from Alec Station. Diane makes an important discovery about the owner of the phone number Owhali gave Chesney. O'Neill searches for solace in his faith as his personal and professional lives crumble before him.

The CIA and FBI are on high alert as threats surrounding the new millennium abound. O’Neill and Soufan raid an AQ cell in Brooklyn. The CIA continues to hide vital information from the FBI while they track suspicious individuals entering the U.S.

O’Neill and Soufan travel to Yemen to begin the investigation into the bombing of the U.S.S. Cole. The FBI becomes aware of a meeting in Malaysia and of Khallad, without knowing the CIA has been aware of both of those things for months.

Everyone adjusts to a new president and, with it, a shift in threat priority. Soufan learns of the importance of UBL’s bodyguard and is refused access to him. O’Neill is denied re-entry into Yemen and forced to resign. The terrorists in the U.S., Hazmi, Mihdhar and Atta, are lost by their U.S. handler.

The CIA becomes aware that Hazmi and Mihdhar are gone and must relay that to the FBI. O’Neill accepts a job as head of security at the World Trade Center. Soufan is sent back to Yemen. Hazmi, Mihdhar and Atta head to Vegas for a final indulgence.

Nobody can get a hold of O'Neill on Sept. 11, 2001; Soufan's evacuation from Yemen stops short as the CIA Station Chief gives him the answers he has been seeking from the CIA; Schmidt is reinstated into Alec Station; Soufan interrogates Abu Jandal.