In a deep underground bunker called 'The Vault' located somewhere in Washington D.C. a group of CIA, FBI and NSA agents work together as part of the USA Homeland Security Force to keep the America safe from terrorists and other threats that the US President receives in a series of classified documents code titled the 'Threat Matrix'. The leader of this unit is Special Agent John Kilmer, a brilliant 42-year-old former FBI agent whom has White House authorization to call upon the technical skills, firepower and the specialist agents. Kilmer reports only to Colonel Roger...
Kilmer and his team travel to Iraq to investigate the disappearance of a former Republican Guard chemical weapons specialist who may be plotting a terrorist attack in the USA on American troops before they can be deployed to the country in the continuing conflict against the Iraqi insurgents.
Kilmer, Frankie, Lark, Vargas and the team investigate the mysterious deaths of a group of people whom were sleeper agents whom are currently plotting to release a deadly germ warfare virus. The team races against the clock to find three infected young people whom have been unknowingly infected which they could kill thousands of Americans if they are not stopped.
Kilmer, Frankie, Vargas and the rest of the team investigate a series of bombings at local universities and must find the culprit before he can strike again. While assisting with the case, Mo is forced to investigate an old friend from Egypt and use the powers of the Patriot Act to detain and interrogate when suspicion falls on him.
Kilmer and the team learns that an old cargo plane that was stolen out of Africa is now filled with old Soviet nuclear waste and being flown by two African AQ terrorists towards the USA on a suicide mission to strike an unknown target. Will the team be able to find the plane and stop it before it crashes into its target?
Frankie roughly interrogates a terrorist at Guantanmo in an attempt to stop the assassination of a major political figure, but in the process the terrorist dies and Frankie is put on trial. Kilmer and the team must look through the video tapes and see if they can stop the assassin and clear Frankie.
When a mysterious sniper begins killing people in San Diego from great distances and the FBI is unable to find the culprit, Kilmer and the Threat Matrix team flies out to California to try to identify the sniper and figure out his motive as well as a way to stop him before he kills more people.
When several dead people are found to have died mysteriously from an unknown virus, Colonel Atkins has Kilmer and Frankie investigate and they learn that the Russian mafia is plotting an biological outbreak using poisoned money from old KGB agents to spread all over the country to destroy the US currency policy.
When the Threat Maxtrix team learns that a notorious arms dealer, named Frederic Vorn, will be coming to the USA to sell some lethal weapons, Kilmer has Mo go undercover to try to buy the weapons before they fall into the wrong hands. Meanwhile, Atkins meets with an old flame, named Senator Lily Randolph, for help in finding Vorn hoping it will lead the team to his other terrorist clients, but Atkins is eventually betrayed by Lily who wants to use the capture of Vorn for her own political gain.
A United Nations team travels to Mexico to investigate a bank that is suspected to be to be laundering drug money for a local cartel. Frankie goes undercover as part of the team. But when cartel terrorists take over the bank, Kilmer, Atkins, and the team makes a secret alliance with a Mexican official to try and save Frankie's life which is in grave danger.
The team suffers an emotional setback when Vargas is killed while on a mission to stop the North Korean's prime minister's daughter from being kidnapped while in the USA to sign an important disarmament treaty. Kilmer and Frankie must find the culprits plotting to carry out the abduction before it leads to a further deteriorate of relations between the two Cold War countries.
When the team breaks into a chemical plant to stop a hostage situation, it leads to a shooting and the entire Threat Maxrix team is put on trial by Homeland Security. Frankie must team up with Homeland Security agent Anders to try to prove that the team did the right thing, while Kilmer becomes uncomfortable about his ex-wife spending more time with her latest interest.