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.

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

In an effort to learn the truth about his brother's mysterious death, Matt begins piecing together clues and finally forces his superiors to tell him the truth. As Matt begins to gather information about his brother Eric's final mission abroad, he poses painful questions about the mysterious death to his parents and finally forces Jackson, Carl and Director Pierce to explain the circumstances so he can get Eric's body back for a proper burial. Meanwhile, Jackson, Terri and Joshua are working to entrap an Indian Intelligence Bureau double-agent working for his own country against the CIA to acquire a submarine capable of launching nuclear weapons.

The CIA conducts an internal investigation when it suspects Jackson of leaking sensitive information. In order to test Jackson's loyalty to the CIA, Matt and Carl secretly recruit the Persian cellist with whom he is romantically involved to gain information about a terrorist threat at the Yemeni embassy. Meanwhile, Terri must forge a 50-year-old document implicating the CIA in illegal activity involving the Dalai Lama that would prove calamitous for present-day Tibet should it fall into Chinese possession.

Matt and Terri learn about shipment. The CIA gets a new cheif.

The agency is trying to find out the if the creator of the super virus is guilty because several people have died to the virus having thought to been sold. Stiles travels to Mexico City to see if the scientist is guilty. Stiles needs to find out where the virus is made, Stiles who came to Mexico begins to believe the scientist is innocent. Stiles enters the lab and finds a lot of empty vials. Gage finds out that scientist's records list 75 vials as well as 73 in the lab that don't contain the virus. They believe one of the scientist family members has the vial with the virus. Haisley learns that Stiles and Teri may have the wrong man. Stiles learns the scientist may have been making a vaccine for the virus.

When Gage discovers that a potential Iraqi defector has been held prisoner in the U.S. for the last 6 years, he authorizes a mission to take the man back to his homeland to identify a weapons site.

When the CIA misidentifies a missionary plane in Colombian drug-trafficking airspace and the Colombians shoot it down, Director Pierce must try to clean up the mess, while the former CIA director tempts Carl to betray Pierce. Meanwhile, Matt and Lisa must contend with a dead body when a foreign agent dies while attempting to sell the CIA classified information.

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.

The Agency discovers that a suicide bomber responsible for the death of 14 people in an amusment park is an American citizen belonging to a terrorist ring.

After unearthing a secret plot by Castro's own men to assassinate him, the agents rush to thwart the plan in order to prevent the U.S. from being framed for his murder.

After the young son of a British Intelligence officer is kidnapped and the man fails to report him missing, the CIA and British Intelligence's investigation takes an unusual turn. They learn that the man didn't report his child missing because the kidnappers are Iraqis and he has arranged to trade plans for an Allied invasion of Iraq in exchange for his son's return. Matt and Carl join the investigators in London to ensure that the officer's plan is derailed without losing the boy in the process. Meanwhile, Robert Quinn, who is temporarily replacing Director Pierce, starts implementing changes. Daniel Benzali (""Murder One"") guest stars.

Is Gage wanted by the FBI? The agents think so,there about to find what he is really up to.

Stiles tries to stop a drug dealer from helping terrorists, Can Stiles get the drug dealer to help capture the terrorists?

The local governor plans a political coup after some American miners are taken hostage in Indonesia.

A CIA Agent is taken Hostage.

After the daughter of the United States Ambassador to Greece is kidnapped by terrorists, Matt and Jackson attempt to track her down. Following the abduction, the CIA reveals to the ambassador that the young woman has actually been working undercover for them for several years. Matt and Jackson think they have successfully rescued her, but then realize they have an imposter and must save the real girl before she is murdered. Meanwhile, Robert uses Lisa to get important information from Patrice, which he turns against her.

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.

Terri,Stiles & Lex must go to Spain to find out why military wives were killed, While Lex, Stiles, & Terri try to stay out of danger.

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Terri, Stiles and Lex oversee the formation of a new Afghan Ministry of Intelligence in Kabul, Afghanistan, where Terri and Stiles' lives are threatened. Meanwhile, Gage deals with a new Afghan Intelligence Minister with a shaky past

A ambitious journalist plans to run a career-making story about one of the Agency's great Cold War successes, which will expose and therefore cost the life of a now retired Russian general who risked his life to help Director Pierce and the CIA. The journalist refuses to kill the story, and Director Pierce and his team must do everything they can to protect the Russian, even if it means putting another life in jeopardy. Meanwhile, Terri's estranged husband begins divorce proceedings, and Matt pushes Jackson for answers about his brother's mysterious death.

The president's brother is in an accident, which put the CIA in a bind.

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

CIA tries to uncover if someone has sneaked a Russian atomic bomb into the US.