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. Sean Hannity guest stars as himself. The titular character, played by British actress Marina Sirtis, was possibly based on the real "Dr. Germ," Rihab Taha, the head of Saddam Hussein's bioweapons program.

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.

A sniper is loose in the city, and the Threat matrix team is trying to profile and locate the killer before he strikes again.

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 goes undercover to set up a deadly international arms dealer who is scheduled to be delivering his wares on U.S. soil

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.

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.

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 A terrorist associated with Al Qaida 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 to disarm the deadly bomb that was set, 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.

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.