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Chief of the FBI's counterterrorism unit, John O'Neill, invites rookie Muslim-American agent, Ali Soufan, onto his squad. Fighting to get information from the CIA, they soon realize their work is just beginning as US embassies are bombed.

Following the simultaneous embassy bombings in Kenya and Tanzania, the FBI begins its investigation on the ground 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, while 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 al-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 al-Qaeda cell in New York City. The CIA continues to hide vital information from the FBI while they track suspicious individuals entering the US.

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

The CIA becomes aware that Al-Hazmi and Al-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. Al-Hazmi, Al-Mihdhar, and Atta head to Las Vegas for a final indulgence.

Vince continues asking for permission to share Al-Mihdhar's visa with the FBI. O'Neill loses his briefcase and an investigation into his handling of classified materials begins. A boy, radicalized after the CIA's retaliation attack killed his friend, travels 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.

It is September 11, 2001 and no one can get a hold of O'Neill. Soufan's evacuation from Yemen stops short as the CIA station chief gives him all the answers he has been asking from the CIA for months. Schmidt is reinstated into Alec Station. Soufan finally interrogates Abu Jandal.