A plot to disperse the plague in an American City is discovered by Bobby and his team. JT pulls together a Red Team to try and discover where this terrorist action will occur before it happens. Sonny gets a promotion.
A female American lawyer is determined to bring in a man who raped several women in his country, and has been assigned some American soldiers to protect her. When the leader is killed when an attempt is made on her life, J.T. is sent to replace him and is assigned to find the man who killed his predecessor. In the meantime newly appointed Sonny has a hard time getting support from the other Joint Chiefs because she's not military.
When an American General in Spain in abducted. J.T. who's just been promoted to Lt. Colonel, wants to go there and try and find him. But he's warned that the Spaniards might not like them walking around, doing what they please. But he goes anyway.
When J.T.'s mission is blown because the country he was in found out about it and threw them out. He suspects that someone within the E-Ring could be leaking the information. So with the FBI they try to find out who is doing it. Sonny tells him not to tell anyone and that includes McNulty.
A plane with some medical missionaries is en route to Venezuela when it is shot down. J.T. and his team are sent to rescue them. Later it is discovered that the Venezuelans believe one of the missionaries is an assassin sent to murder the President, so some Venezuelans are sent to find them and if they're caught will be subjected to torture. But Sonny later learns that the Venezuelans' suspicions are not without merit so she tries to find out what's going on.
A US submarine crashes into a North Korean sub in their waters. Despite protest from people at the Pentagon, Bobby and the crew mount a rescue of the enemy crew. Back in DC, JT meets a new girl who has unknown Pentagon connections.
J.T. and Bobby are in Saudi Arabia meeting with a prince who is married to an American. While there, their children are kidnapped. At first they believe it was enemies of the royal family. But when J.T. finds them he discovers that the kidnappers are American and they were hired by the princess who's become disenchanted with the life she chose, and that the prince has promised their daughter to someone even though she's only a teen. J.T. brings them back to the palace but because he is in an embassy vehicle, he gets the princess to come with him. After arriving at the...
When American soldiers are attacked in Iraq, a Congressman who wants to pull Americans out is poised to do it. But Sonny sends J.T. to train Iraqis in the art of protection. When J.T. chooses his team, he picks one of them to be the team leader. But the man's brother who is in league with some insurgents plans to attack the base using his brother.