Colonel McNulty finds himself at odds with Major Jim Tisnewski. The major must convince his superiors at the Pentagon and the Joint Chiefs of Staff that the United States should risk war with China to rescue an American operative.

The Pentagon receives word that a terrorist ally surfaced in Uzbekistan. McNulty and his staff must move quickly to capture him while they have the opportunity to do so. Meanwhile, JT has a run in with Samantha Liston, a woman from his past who now ranks above him. As the mission is set for Uzbekistan, JT must send his old unit into harm's way.

McNulty sends JT on a mission to Iraq to find out why there is unauthorized covert action and if the United States is illegally treading on Iranian soil . However, he winds up wounded and is forced on the run. Sonny and Algazi assemble a team to rescue JT from Iraq. McNulty gets charged with sexual harassment by the Inspector General.

A repeat genocide is threatened when machetes are uncovered in Burundi, Africa. As the tensions between Hutu and Tutsi groups escalate, JT must deal with the politics of the Pentagon to get help to the region in time.

Two US Marines are accused of raping a young local woman in Surinam. JT learns of this and he immediately jumps to action only to find opposition from above. The United States doesn't want to jeopardize it's aluminum interests controlled by the Surinamese government. He must navigate the political maze to discern the truth and try to save the soldiers' lives.

The CIA unexpectedly puts a terrorist on the capture/kill list and JT digs into the reasoning behind it. He soon finds that not everything is as expected so he challenges his superiors but finds that Pentagon politics can be deadly if you're not careful.

JT's girlfriend, Angie, is put in a risky situation and only leaves JT one clue as to what happened to her. Using his past Special Ops experience, JT must find what has happened to her.

In Columbia, JT is heading an undercover operation to nail the drug lord who attacked Angie. Now he has to finish a job they started together years ago.
Back in the Pentagon, Sam finds evidence on the CIA director and has him indicted.

JT and a SO team are sent to Detroit to address a situation with a radical Christian group that has taken over a mosque and taken hostages. Sonny must address legal concerns around the action due to FBI jurisdiction and the Posse Comitatus act.

McNulty discovers that a captured Navy Seal could be alive and he and JT are set to save the man. However, they soon face resistance from the Pentagon and might have to do what is known as a "backdoor" mission to save the soldier. Also, more about McNulty's mysterious past is revealed during this endeavor.

On Christmas Eve, JT works on a humanitarian aid mission for an Afghanistan village that helped Delta several years ago. He finds the village confronting bad weather and an advancing Taliban force. Also, Sonny helps JT's father who needs a favor.

A interagency strike in Amsterdam uncovers an illegal lab manufacturing the plague, which sents JT and his team into action, planning an anti-terrorism strike. But as they plan, they discover the threat is closer to home then they had thought.

JT and Special Ops get involved in investigating possible war crimes during actions in Sarajevo.

JT celebrates his promotion to Colonel as word is received that a Spanish special ops officer was kidnapped. The team travels across the globe to track down those responsible.

A mission in Pakistan fails, forcing JT to go inside E-Ring in search of a mole.

A plane carrying American doctors on a mercy mission crashes in the Venezuelan jungle. The Venezuelans claim they were on a mission to assasinate their president. JT and his team must rescue them before they are captured.

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 tohug everyone aboard rather than allowing the Americans to get their hands on the Korean submarine.

While visiting Riyadh in Saudi Arabia, JT and Bobby become involved in a scheme to kidnap the two daughters of the crown prince to help them to return to the US where they grew up.

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 sleeping 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 has to undergo a psychological evaluation. As he is examined, he recounts a Lebanon mission set up to save one of his men who was tortured by insurgents.

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 hugging 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.