An assassination attempt on Lisa strikes Matt instead and leaves him hospitalized and fighting for his life. While Robert tries to hide the events from the press, Jackson is forced to work with the chief of counterintelligence to determine who ordered the attack on Lisa and how her position at the CIA was uncovered. Eventually, Lex admits to indirectly blowing Lisa's cover to the assassin and, in the process, unknowingly giving him access to information on Lisa. However, Lex soon redeems himself by leading Robert and Jackson to the terrorist organization behind the shooting. As Matt hangs on to his life by a thread, Lisa contemplates a leave of absence from the CIA.

On his first day as the new Director of the CIA, former Senator Tom Gage is immediately confronted with a high-profile crisis when the Agency is linked to the death of a young Vietnamese man in Washington D.C. As Tom works with Jackson and Carl to learn how the CIA was involved, he discovers that when Robert was acting as the director of the CIA, his secret negotiations with a Middle Eastern prince were directly responsible for the Vietnamese man's murder. Tom must find a way to hide the Agency's involvement without implicating an innocent man for the crime. Meanwhile, Terri runs into a photographer whom she realizes is linked to a radical pro-life group that has bombed abortion clinics.

Tom and Carl learn that a story about a war crime Tom allegedly committed during his service in Vietnam is about to be revealed in the press and that the source of the story has been found dead. Meanwhile, Matt and Jackson receive word that a visiting Eastern European dictator is near death and they enlist a hooker to help determine how ill he really is. At the same time, Joshua must deal with a museum curator when he accidentally destroys a cow costume that's part of an upcoming exhibit.

After a CIA agent is murdered, the agency joins with the police department of Washington, D.C. to investigate his murder.

Agents of the CIA go to France to find Matt's killer. When the Secret Service, CIA, FBI, and INS fail to inform each other, Robert Quinn forms an Incident Response Team to work with the CIA, FBI, Secret Service and INS.

Teri is taken to Stiles to his home. The Incident Response Team heads to Ireland to stop arms dealers.

Lex learns that a possible bomb attack may occur in Australia, Gage doesn't want to act because terrorists may another attcak on the U.S.