As Mack and Tiffy uneasily proceed with plans to leave Unit life behind, Mack's former team members are out in the field dealing with struggles of their own. After carrying out one mission to intercept a package in Pakistan, the Unit must regroup and focus on executing a second mission in order to stop a plan to spread a deadly disease throughout the western world. Meanwhile, when Tiffy helps a student in need, she realizes the true impact of leaving the Unit. Also on the home front, Kim and Bob welcome a new addition to their family.

Jonas and his team carry out a complex and dangerous prison escape of a rogue former Unit operator in order to have him help track down the world's leading arms dealer. Meanwhile, in desperate need of money to care for her aging mother, Molly takes a one time recruiting job to hire someone away from the military, but some members of the Unit family are not happy about her decision.

Jonas and his team are sent to Paraguay to eliminate a militia rebel leader, but the mission is put on hold when they must rescue two Charlie team members trapped by a sniper. Meanwhile, Kim and Molly help the fianc of a fallen member deal with her loss, and Kim urges Bob to sign a life insurance policy when she sees how little the army does to help the widows of men who have served.

The Unit tracks down a wanted Indonesian terrorist on U.S. soil, but in a race against time they must prevent his moving target from exploding. Meanwhile, the Unit wives are concerned that a stranger is putting their families in danger.

A mission to extract a West African dictator from a U.S. hospital during a hurricane seems to be a fairly straightforward assignment under adverse conditions, but when the Unit discovers that 10 patients were left behind during the hospital evacuation, they must choose between saving the dictator or the patients. Meanwhile, Tiffy and Mack get busy working on becoming pregnant, and Molly's recruit, Jeremy, comes home thirsting for more action out in the field.

Jonas poses as a diamond merchant in Africa, where he and his crew set their sights on tracking a terrorist. Back home, Molly and the other wives prepare for an annual base reunion and discover an undelivered love letter written by a soldier to his wife shortly before he was killed in action in 1944. They attempt to find the widow and deliver the letter to her. Also, Tiffy disrupts a peace rally and defends her views on warfare.

Jonas involves Bob in a non-work related mission to save Ron Cheals' illegitimate daughter from a cult, but Jonas' favor for a friend puts the two Unit members in jeopardy of losing their jobs, their reputations and more. Meanwhile, Tiffy helps out Charlotte Ryan when she takes responsibility for her reckless driving; however, Tiffy's good intentions may prove disastrous for both the Unit and her marriage.

Bob and his translator survive a helicopter crash in Siberia but now, cut off completely from civilization and without their gear, they face the challenge of enduring the harsh weather.

Jonas works closely with his undercover wife to assassinate a prominent Latin American official who threatens the U.S. oil supply. However, after Colonel Tom Ryan is questioned about the Unit's current mission in a congressional briefing in Washington, a subsequent press leak undermines the mission and puts Ryan's men in danger.

Jonas is captured by a militia group during a mission and held hostage. He's forced to make a video that outlines the group's demands. The chief one is that a terrorist held by the U.S. be released within 48 hours or Jonas will be executed. The suits in Washington, D.C., refuse to negotiate, so Col. Ryan sends his own men in to attempt a rescue. Back at the base, Tiffy learns she may face time in prison for her involvement in covering up Charlotte's reckless driving.

When Jonas' family gathers for a long overdue celebration honoring his dad, Jonas witnesses some disturbing behavior by his nephew who just returned from combat and he attempts to put a stop to it. Meanwhile, Mack has to deal with a plane that has flown into a restricted area and identify the mysterious passenger on board.

When the Unit is assigned protection detail for a U.S. Senator traveling in a hostile country in Asia, Jonas is given his own top secret assignment within the mission from the President of the United States.

The Unit's dangerous mission in North Korea is jeopardized when a spy overhears Kim Brown talking about intimate details of the operation.

The Unit is assigned to slip into Iran to plant radiation sniffers, but when things go awry, Mack must decide whether to leave the Iranian woman who served as a guide behind and face torture or kill her himself.

Jonas and his crew, on a mission to protect a Middle Eastern dignitary at the United Nations, must diffuse a bomb found in the office of the U.N. secretary general. Meanwhile, Molly and Tiffy visit Vietnam for a ceremony to honor those who fought there. While there, they try to locate a onetime POW. Their search is prompted by a visit from the man's mother, who believes her missing son is still alive. Back at home, Crystal tries to seduce Mack and threatens to tell Tiffy about them.

While in Germany for some friendly competition with Special Forces teams from various nations, the Unit discovers there is an outside entity involved and they must prevent a real terrorist attack from happening.

At a remote Army base in Afghanistan, Jonas and the unit discover that the base is in total mayhem and are forced to take control of the base. In doing so, the unit must organize the troops in order to fight against the tribal militia surrounding the base.

When Jonas and members of the Unit study advanced desert warfare in Israel, Grey becomes smitten with an Israeli soldier, but the relationship proves deadly.

Brown and Williams enter into a world of voodoo when they travel to Papua New Guinea to retrieve a black box from a downed special-forces aircraft. Back at the base, Mack learns that Crystal is giving information to a reporter and he tries to stop her.

When a prominent school in Virginia is taken over by gunmen, The Unit is called in to assist the SWAT team. Their main goal is to free the hostages before anyone is injured. The son of an officer shows interest in Lissy, but the situation is complicated when Kim defies Tiffy's order and it's Lissy who gets the punishment.

Bob's loyalty is challenged when he joins the CIA for a covert mission that could put the Unit in jeopardy. Back at the base, Mack becomes convinced that Tiffy is having an affair.

Mack, Grey and Williams protect a Thai prince on American soil and uncover scandalous family secrets that include murder. Meanwhile, Bob's life is endangered when a parachute jump goes awry.

The second season concludes with the Unit being investigated by a government agency that is probing into possible infractions that could result in criminal charges.