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.

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.

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.