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.

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.

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.