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.

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.