John O'Neill, the chief of the FBI's counter-terrorism unit, invites rookie agent Ali Soufan, a Muslim-American, onto his squad; they soon realize that their work is just the beginning when two American embassies are bombed.
Following the simultaneous embassy bombings in Kenya and Tanzania, the FBI begins a ground investigation while the CIA starts working on a retaliation plan.
The FBI finds one of the surviving terrorists and discovers a game-changing lead in Nairobi; the CIA's retaliation plan is approved.
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 Chensey; O'Neill searches for solace in his faith.
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.
Vince continues asking for permission to share Mihdhar's visa with the FBI; O'Neill loses his briefcase and an investigation into his handling of classified materials begins; a radicalized boy goes to Yemen to start his own martyrdom journey.
O'Neill and Soufan travel to Yemen to begin the investigation into the bombing of the USS 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 the importance of UBL's bodyguard; O'Neill is denied re-entry into Yemen and forced to resign; the terrorists in the U.S. are lost by their 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.