When the homeland security team goes after a serial bomber who has been targeting universities, Mo ends up investigating his childhood best-friend, Amir Abadiyah, who is now a professor at the first university to be bombed. Because he donates regularly to a charity that is on a list of organizations that are suspected to have terrorist ties and doesn't have an alibi to clear him of suspicion, the Patriot Act is invoked and the professor is taken out of his classroom and held for questioning.
A message that the bomber sent to the Times is found. It demands that they publish a graduate thesis from 1986. The thesis was written by a man who is now also a teacher. Kilmer invokes the Patriot Act and has the man (Prokop) taken from his home for questioning.
Clearly, Mr. Prokop is not the bomber, but after the Threat Matrix team barely manages to evacuate the next bomb site in time, it is discovered that Prokop has a younger, mentally unstable, brother who was presumed dead ... but isn't. With Prokop's help, the team finds out where the next bomb will be placed and races there - apprehending Prokop's brother and preventing the blast from taking place in a crowded university football stadium, on the opening day of the season.
At the end, Mo feels badly because his friend was up for tenure, and by having him taken for questioning with no explanation, he has probably ruined Amir's career. Kilmer tells him that the world has changed, and we aren't children anymore. They're on the roof and the sun is setting. Kilmer leaves and Mo knees down on his rug to begin his evening prayers.