In North Korean waters, a submarine that Bobby's team is on collides with a North Korean nuclear submarine, damaging it. The Korean commander is eager for the Americans to save his crew, but he must work against his own countrymen, who have sent another vessel to kill everyone aboard rather than allowing the Americans to get their hands on the Korean submarine.

On a mission to train an elite Iraqi secret service unit, JT and Bobby befriend an Iraqi soldier who doesn't know his brother is a suicide bomber fighting against the American occupation. Meanwhile, Sam accompanies a Congressional delegation to Iraq and becomes trapped by the bomber on a military base with JT and Bobby.

JT and the team travel to Mexico to apprehend a drug lord who has allied himself with Al Qaeda and is smuggling terrorists into the US. Meanwhile Bobby receives some bad news.

After escaping from the hands of Mexican Police following a doomed operation, JT and his team end up killing a drug gang and a federal agent on the American side of the border. As the team was debriefing in a Miami hotel, Sonny and McNulty were trying to solve the crisis started by a mole inside the Pentagon.