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.

Kilmer goes to Cambodia and finds trails of his father who went MIA during the Vietnam War. Kilmer tracks down a friend of his father's and learns that his father is dead.

When a prisoner requesting asylum informs the U.S. government that a shipping container with a cell of terrorists has set sail for U.S. soil, Frankie is sent in search of the truth. Back at the "Vault" in Fort Meade, Kilmer's team is at work on the mission, but after it goes awry and Frankie goes on the run in Jakarta, Kilmer is torn between his concern for his ex-wife and the protocol he's sworn to keep.

The ultimate consequences of domestic drug abuse become much clearer when Kilmer and the team discover a Vietnam veteran and DEA Agent who are dealing and using crystal meth from a small, local lab.

Germ warfare becomes personal when Kilmer risks exposure to an extremely deadly gas in order to stop a widespread catastrophe.

When a trio of young renegades sets out for Las Vegas carrying a highly communicable and deadly virus, Kilmer's team risks exposure to the outbreak to stop them from reaching their destination.

Kilmer and his team search for a domestic terrorist bomber who is targeting several large universities. But when Mo's lifelong friend, Amir, is named as a suspect and his career is placed in jeopardy, Mo is forced to question his own choices, as well as the viability of the Patriot Act.

The Team must work together in Africa and stateside in order to prevent an airliner filled with deadly nuclear waste from crashing into the East Coast of the United States.

In an effort to stop an assassination attempt on a major political figure, Frankie interrogates the one man who knows the potential suspect's identity. When her detainee dies in custody, it's up to Kilmer to find the would-be murderer in order to clear Frankie's name.

When a crazed sniper goes on a killing spree in San Diego, the Threat Matrix team works with the FBI to stop the surprisingly young, troubled shooter.

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.

Mo plays the roll of double agent in order to apprehend a small arms dealer who is moving missiles on to U.S. soil. Meanwhile, Atkins' trust is betrayed by a Senator holding court during an election year.

A bank hold-up in Mexico forces the team and the ambassador of Mexico to work together when secret alliances create a deadly situation that puts Frankie's life in real peril.

One of the Threat Matrix team is killed in an attempt to prevent the North Korean Prime Minister's daughter from being kidnapped.

Kilmer and the team try to stop a terrorist and his young daughter before they leave the country and to disarm a potentially deadly bomb before irreparable damage is done.

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.