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Kilmer goes to Cambodia and finds trails of his father who went MIA during the Vietnam War. Kilmer tracks down a friend of his fathers and learns that his father is dead.
The team infiltrates a chemical plant they suspect of being the target of a terrorist attack. A shootout takes place and then the Homeland Security team is put on trial. Frankie, with the help of some other agents, cross the line and do an investigation of their own.
In order to avert a deadly radioactive blast, the Threat Matrix team has to work with an unsure suspect to identify terrorists who, after plastic surgery, now have new faces.
A terrorist associated with Al-Qaeda attempts to flee the country with his daughter after setting the wheels in motion for a deadly disaster. Kilmer and the team attempt to stop them and disarm the deadly bomb that was set, before irreparable damage is done.
The aide to the North Korean Deputy Foreign Minister (who is also his illegitimate daughter), is kidnapped by Korean drug dealers, who want to use her as leverage to influence the Foreign Minister's decisions. Almost rescued at the moment of her kidnapping by Tim Vargas, she is ultimately set free by Kilmer and undercover DEA agent Danny Roh.
A combined United Nations/Threat Matrix operation to audit a Mexican bank suspected of funneling money to Al Qaida turns dangerous when the bank is robbed and Frankie's life ends up in danger.
Mo goes undercover to set up a deadly international arms dealer who is scheduled to be delivering his wares on U.S. soil
Atkins is reunited with a Russian agent and an American double agent from his past when the team attempts to prevent poisoned money from reaching wide circulation.
A sniper is loose in the city, and the Threat matrix team is trying to profile and locate the killer before he strikes again.
Considered an enemy combatant, a French-Algerian man is detained at Guantanamo Bay, Cuba. Because Frankie refuses to allow him to see a doctor while she is interrogating him, even after he tells her three times that he needs to see one, the man suffers a heart attack and dies. Whether it was because he was unwilling or unable, the Algerian national never directly gave Frankie any of the information she was trying to get before he died, and she ends up in a courtroom, first disobeying the order to quietly accept a plea bargain, in order to keep the entire incident below the radar, then pleading "not guilty" to the charge of second degree murder, which means that the matter goes to trial. With Mo's help, Kilmer ends up saving Frankie from going to jail by using the information that was gained before the sleeper-agent died, to stop an assassination attempt that might have started a war in the Middle East, and then testifying in court about it on Frankie's behalf. As a result, Frankie is acquitted.
A corrupt West Africian airport official and a CIA agent who has changed sides as a result of the role that the U.S. played in Angola end up being key components in the theft of an airplane that is used to attempt an act of terrorism on the east coast of the United States.
When the homeland security team goes after a serial bomber who has been targeting universities, Mo ends up investigating his childhood best-friend, Amir Abadiyah, who is now a professor at the first university to be bombed.
A dog from the Congo, infected with a new strain of Ebola, ends up in Amarillo, Texas. Because the daughter (Hannah) of the pet and feed store owner who ordered and received the dog is a cocktail waitress at a popular local bar, she ends up exposing dozens of people to the virus in one night. Although the outbreak is a natural one, the homeland security team takes charge, to prevent it from spreading. Their job is complicated by the fact that on the night that Hannah infected everyone, she and her ex-convict boyfriend (Shane) leave Amarillo and head to Las Vegas Nevada, where they plan to be married.
The team heads to Iraq to investigate the disappearance of a Bio weapons scientist who is suspected of planning an attack in the US. They eventually catch up with her in the US but she has already passed the weapon on.
The team investigates a drug connection to international terrorists and must stop them before they detonate a bomb on veterans day.
The team must stop a bomber detonating a bomb at the G8 leaders summit meanwhile Frankie is kidnapped in Jakarta after trying to get information to stop the attacks.
