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.

Africa is experiencing another threat of genocide reminiscent of Rwanda and JT seeks the help of a bureaucrat to help out before time runs out.

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.

When JT challenges his superiors' reasons for unexpectedly placing a known terrorist on the capture/kill list, he learns that politics in the Pentagon can be deadly.

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.

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.