List of The Agency episodes

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.

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

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

The CIA and the FBI learn a New Jersey man who was murdered was a former Russian spy (sleeper agent) with a suitcase nuke hidden underground in his backyard fallout shelter for more than a decade. Also, Terri's ex husband hires a detective to gather information on her for their divorce.

When an agent dies in the line of duty, the CIA learns of an impending terrorist attack somewhere in Europe. Matt tries to convince a Syrian diplomat to divulge information about the location of the attack, but he'll only cooperate if his family is brought safely to the U.S. Note: This episode was written in March 2001 and filmed as the series premiere once CBS picked up the show for the 2001-02 season; it was moved further down into the Season 1 order so that it had distance from the 9/11 attacks.

A terrorist uses anthrax as a biological weapon to murder two Belgian kennel owners and more than 20 dogs, which leads Matt to suspect the killer will strike again on a larger scale.

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 Haisley (Will Patton), Carl Reese (Rocky Carroll) 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.

When the National Security Agency (NSA) learns of a plot to assassinate the King of Saudi Arabia, Matt and Lisa help track down those involved only to discover that there is a larger terrorist plot in the works. Soon after Matt and Lisa catch the would-be assassins, Israeli intelligence informs the CIA that one of the incarcerated terrorists is their own agent on an undercover mission and requests his safe return. Once Matt arranges this, the Agency discovers that Israeli intelligence has deceived them and the man they released is a link to a terrorist they had been pursuing for years.

An 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.

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 did not 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 guest stars.

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 impostor 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.

An assassination attempt on Lisa strikes Matt instead and leaves him hospitalized and fighting for his life, while the CIA investigates the ugly white guy who shot her. 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. While Lex admits that he accidentally tipped off the shooter to Lisa's identity, he redeems himself by uncovering information that the white guy shooter was a neo-Nazi who was working with fanatics in Pakistan to form a new Jihadist-Nazi alliance against world Jewry. As Matt hangs on to his life by a thread, Lisa contemplates a leave of absence from the CIA.

Matt and Terri go to Belarus to gather information about an arms shipment to Iraq. When Terri discovers Matt is in danger, she blows her cover to save him and the mission, and winds up a prisoner herself. Senator Tom Gage joins the agency as the new director.

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 anti-abortion group that has bombed women's health clinics.

The CIA tracks an Algerian suicide bomber as he enters the U.S., but the agents do not realize he is infected with smallpox until he is taken into custody. When they learn his mission is to infect the Agency first, the agents race to ensure the virus is contained before more people are infected.

A former corporal who served under Gage in Vietnam accuses him of committing a war crime that involved murdering civilians. Meanwhile, Matt and Jackson receive word that a visiting Eastern European dictator is near death and they enlist a prostitute 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.

The Agency learns about a chemical weapons plant in the Sudan that must be bombed, although it will put 150 innocent enslaved workers in danger. Jackson devises a plan to save them. Meanwhile, the CIA prepares a memorial service to honor an agent, but Quinn tries to turn it into a media event. Carl and Tom step in to honor the family's request for a quiet tribute.

The chief intelligence officers from India and Pakistan meet with Gage at the Agency's headquarters to head off a nuclear war. Meanwhile, Carl's son visits him and gives his father some disturbing news.

Jackson assumes the identity of an arms dealer so he can try to sell weapons to the Russian mob, and is taken hostage by the mobsters. As the CIA tries to decide how to handle the situation, he develops an odd relationship with his captor and his son. Meanwhile, Lisa Fabrizzi returns from a leave of absence and brings with her some surprising news.

A CIA agent is murdered in Washington and the CIA is forced to join with the police force to find the killer. Chief Jack Mannion (Craig T. Nelson) visits the CIA headquarters to meet with Gage and Quinn to learn what they might be withholding. While Matt and Haisley work with Mannion's team, Detectives Temple Page (Sean Patrick Thomas) and Kevin Debreno (Jonathan LaPaglia) attempt to track down the men responsible.

This episode concludes a crossover with The District that begins on "Shell Game".

When a CIA agent posing as a diplomat is taken hostage in Uzbekistan, Gage sends Matt and Terri to save him. Lisa predicts another terrorist attack will strike D.C., which raises concerns among her co-workers. Jackson's romance disintegrates when his girlfriend believes he's secretly working against the CIA.

CIA agents 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 liaise between all the agencies.

Gage must decide whether a hijacked plane carrying Stiles and Lex should be shot down.

Terri and Stiles receive death threats as they and Lex oversee the formation of a new Afghan Ministry of Intelligence in Kabul, Afghanistan. Meanwhile, Gage deals with the new Afghan Intelligence Minister, who has a shaky past.

When a CIA plane crashes in China, the operatives must hide all the evidence before it is discovered.

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

The Agency discovers that a suicide bomber, responsible for the deaths of 14 people in an amusement park, was an American citizen belonging to a terrorist ring.

A blown operation leads to a Senate inquiry into possible wrongdoings at the CIA. The agency tries to turn a Colombian druglord and terrorist into an informant, but the operation goes awry when a DEA officer tips off the police about the operation, causing the deaths of seven people.

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

When Quinn reports that Stiles is missing, the agents forgo their Thanksgiving plans to help locate him.

Is Gage wanted by the FBI? The agents think so - they're about to discover what he is really up to.

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

Stiles and Terri head to the Gaza Strip in search of a U.S. citizen who left America with his wife following a killing spree at a travel agency.

The CIA plans to publicly discredit a profoundly anti-American Indonesian cleric who is the favorite to become Indonesia's next President, but former U.S. President James Graydon wants to see the election proceed properly.

Lex learns that a possible bomb attack may occur in Australia. Gage doesn't want to act because he is afraid that the terrorists may carry out another attack on the U.S.

Stiles heads to west Africa, to help former CIA informants, and runs into someone he used to love.

Gage goes to Israel to help with peace talks.

Terri, Stiles and Lex try to stay out of danger when they go to Spain to find out why a number of military wives were attacked and/or killed, while an operation at home finds unusual connections between international terrorists and people of high status inside Spain itself.

Stiles tries to stop a drug dealer from helping terrorists. Can Stiles persuade the drug dealer to help capture the terrorists?

A CEO whose firm saw over 200 employees murdered in the 9/11 attacks starts a bloody private war against the Saudi Royal Family, and the CIA has to stop the situation from becoming a global catastrophe.

After several people die from a super virus, the agency tries to find out if the creator of the virus is responsible. Stiles travels to Mexico City to see if the scientist is guilty, but as his investigations proceed, Stiles begins to believe the scientist is innocent. After finding out where the virus is made, Stiles enters the laboratory and finds a lot of empty vials. Gage discovers that the scientist's records list 75 vials in addition to the 73 in the lab that don't contain the virus. They believe one of the scientist's family members is in possession of the vials with the virus. Haisley learns that Stiles and Teri may have the wrong man. Stiles learns the scientist may in fact have been making a vaccine for the virus.

Terri learns that Brian, the man she dated in college, might be a double agent, because his company could be shipping weapons to North Korea, though this may be without his knowledge. Meanwhile, Quinn discovers that his sister is dying. When she commits suicide in her car, he kisses her goodbye. Terri and Stiles continue try to find the guidance system bound for North Korea. Caroline finds out that her husband Brian is under suspicion, and attempts to protect him. When Terri goes to meet Brian and finds him dead, his wife is questioned about whether she'd received bad information, and if she killed him as a result.

As Haisley and Lex's investigation into Terri's abduction reveals more details, Haisley suspects that Joshua may be a double agent. Haisley reports his findings to Quinn, and is shocked by what Quinn tells him. Meanwhile, Stiles' attempt to rescue Terri puts both of them in danger when he is discovered. Her captors are forced to flee with Joshua, but not before detonating the bomb they'd attached to Terri's neck. This episode ends the season, as well as the series, with a cliffhanger that was never resolved.