Newcomer Bob Brown joins Jonas' team as they set out to rescue a hijacked plane filled with European businessmen. Meanwhile, the Unit wives help Bob's wife Kim get acclimated to "unit life" as she struggles with the level of control the Unit has over her personal life. Even though there seems to be a lack of privacy, there are still secrets in the Unit that need to be kept private.
An international terrorist falls prey to the Unit during a mission to Africa to recover a satellite. Jonas and his team, minus Bob Brown, must adapt to the new situation and pursue the terrorist. Back at the base, Bob is questioned by a government official about the Unit's role in the rescue of a hijacked plane. Meanwhile, back on the home front, Molly visits the Unit's psychiatrist and covers for her husband regarding the shooting at their home, and Kim's frustrations about moving are put into perspective when she comforts a woman who has just been notified that her husband died in combat.
A simple rescue mission proves to be extremely difficult for Jonas when two members of the missionary group refuse to leave. Meanwhile, Bob inadvertently shoots Mack during a training exercise and must repeat the drill over and over again, until he gets it right. Also, the Unit’s wives come to the rescue after Col. Ryan fails to convince a visiting Senator of the importance of investing in military training.
The Unit is sent to Los Angeles to protect Mexico's drug minister from an assassination threat. An attempt on the man's life fails, but his wife and two young sons are kidnapped. Back at the base, a former Unit wife returns and tries to lure away Unit members by enticing their wives with opportunities for high-paying contract work in the private sector. Also, Ryan orders Mack to take some time off alone, which doesn't sit well with Tiffy.
The Unit members become personae non gratae after they successfully carryout an assassination on their latest mission in Spain. A resourceful Jonas is able to escape with ease, while Bob’s attempt to flee is filled with numerous complications, including his arrest. Meanwhile, back on the homefront, Jonas and Molly try to convince their daughter not to leave college to enlist in the military.
The Unit is sent on a mission to the Russian embassy in Israel in hopes of recording evidence that the Russians are planning to sell materials to the Iranians that will enable them to build a nuclear bomb. The plan seems doomed from the beginning when Bob is banned from entering the embassy and Jonas seems unable to elude embassy security. Meanwhile, Kim becomes suspicious when she sees Tiffy sneak into a hotel room and, due to security warnings, Kim reports the incident to Tiffy's secret lover, Col. Tom Ryan.
A joint mission to intercept the Taliban leader's convoy is disrupted when Bravo team's helicopter goes down with engine trouble. Jonas is faced with the extremely tough decision of whether to leave the downed helicopter and continue on the mission or rescue the men of Bravo team. Meanwhile, on the home front, Molly is coordinating a dedication ceremony honoring retired Unit member Ron Cheals and discovers that he is struggling with a prescription drug addiction.
Based on the real-life training course that the military uses to prepare for capture by enemy forces, The Unit takes on a grueling exercise of torture and humiliation ("SERE"). The training proves to be especially difficult for Bob, who is sick when the training starts, and the torment pushes him close to death. To complicate matters, the CIA is orchestrating exercises with virtually no limits to the level of physical punishment and emotional manipulation that can be used in an effort to break them, which would result in them being kicked out of The Unit.
After an effort to buy the surface-to-air missiles from a drug lord falls through and the missiles disappear, Jonas and his team must track down the weapons before they are taken out of the country. Jonas bonds with a local boy who directs the team to where the SAMs have been taken to be shipped and now it is in the Unit’s hands to destroy them. Meanwhile on the home front, Kim stirs up more trouble when she insists that the “Family Readiness Group” deals with more serious issues, and Williams struggles with how and when to tell the woman he wants to marry that he is a Unit member and not a clerk on base.
When Bob's cover is blown while training soldiers in Africa, he advises Jonas to cancel a planned visit by a dignitary due to impending danger; however, things get complicated when they learn that the visit is a cover.
Despite warnings of danger, the visiting high ranking official refuses to cancel his plans. Meanwhile, Kim gets an unexpected encounter while working at the radio station and Molly is presented with a real estate investment opportunity.
When Keith Soto, the son of a former Unit member, returns to base for a reunion, Jonas and Col. Tom Ryan discover that he is a newspaper reporter working on a story that threatens the secrecy of the team.
Although perturbed by the fact that Keith uses the reunion on base as his way in to get a story, Jonas decides to tell him the "truth" about how his father was killed under the condition that he promises not to publish the story. Jonas is under extreme pressure to prevent Keith from running the story, for the consequences could be detrimental to the entire Unit. Meanwhile, with Tiffy and Kim's help, Molly manages to track down the woman who scammed $40,000 of the women's investment fund.
The Unit is called in to consult on a bomb planted in an Atlanta bank, but they must take over control when they learn that the bomb might be nuclear.
Jonas and his team take over, but when they hand control back to the bomb squad, the Unit's specific recommendations regrettably are not taken into consideration. Meanwhile, Bob and Kim take a vacation, but Kim soon discovers that Bob has whisked her away on a mission and needs her help.
Despite encountering several obstacles, the Unit detains a former Yugoslav general wanted for war crimes and lets the U.N. take credit for the capture. However, unbeknownst to the team, the criminal escapes U.N. custody and is now seeking revenge on the Unit. Meanwhile, things become unstable at home when Tiffy thinks Mack re-upped with the Unit and Kim learns some disturbing news.
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.
The team is left in shambles as Jonas continues to elude an assassin and Bob may be reporting to another agency. But in the midst of it all, Ryan tries everything to get the team back together.
Jonas works to uncover the conspiracy that tore his team apart. He must find a way to reunite the unit and clear Col. Tom Ryan's, all while keeping his wife, and the other men's wives, from harm or CIA scrutiny.
Now that the team is back together, they all head out to stop a plane with deadly nerve gas from reaching Ft. Griffith. Meanwhile, Kim has to broadcast a fake weather bulletin so that all personnel will take cover.
Bob, Williams and Mack head to Abidjan to rescue Embassy staff and their families. Meanwhile, Jonas' daughter decides to enlist, so Jonas tests her strength and dedication.
The team tries to recover a chip with information on it that could prevent a terrorist attack on the United States. Meanwhile, Kim is placed on bed rest and Bob struggles with taking care of the kids.
Jonas, Mack and Grey are assigned to keep a pop star safe while Bob and an escort from the Justice Department return a prisoner to his home country for execution.
Jonas and Williams must perform emergency surgery on Grey when he is injured during a mission. Later, the team has to cope with a devistating loss.
Jonas seeks to avenge the death of one of their own; Brown works with a journalist to make sure The Unit isn't betrayed by him; and the team comes together to cope with Williams' death.
Grey goes undercover to gather information on gang members who are stealing explosives that may possibly end up in the wrong hands.
Bob wrestles with a moral conflict during a sniper mission. Elsewhere, Tiffy and Kim discover some surprising information about Molly.
In London, Jonas teams up with a British MI5 agent who is suspected of collusion with a Russian scientist they are tracking. Jonas’s assignment to discern his partner’s loyalty is complicated by the fact that Jonas once had been engaged to the man’s wife.
While women are being secretly relocated and moved off the base for their own safety, Jonas and the team must unravel an assassination plot against the vice president and president elect.
The team follows a scientist on a commercial flight who they believe will be the next target of terrorists they hope to link to a presidential assassination plot at the same time as their wives are relocated and given new identities back home.
Jonas vows to help save a group of girls who are being trafficked as sex slaves by the man he hopes will lead the team to a nuclear weapons smuggler they are trying to find.
Bob is undercover as a scientist when he's kidnapped by a drugs cartel. They want him to help them to disguise cocaine. Mack is als undercover somewhere as a prizefighter.
A nuclear scientist insists on making a deal with the team before he will reveal vital information about a terrorist attack in a major U.S. city.
Back home, Molly, Kim and Tiffy are drafted into service to work undercover with Jonas
The team produces fake evidence of an attack to con a terrorist into exposing his accomplices before the truth comes out and they can get away.
Mack wants Tiffy to reveal details about her relationship with Ryan.
Part 1 of 2. Jonas' daughter, Betsy, is kidnapped in Iraq, and he and the team go in to rescue her.
Back at home, Mack plots his revenge against Ryan for having an affair with Tiffy.
Part 2 of 2 Jonas and the team attempt to rescue Jonas' daughter, Betsy, from her kidnappers. Back at home, Mack has a chance to carry out his revenge against Ryan for his affair with Tiffy.
Jonas and his team attempt to keep a truce intact between two warring Afghanistan tribes by delivering a bride to her groom, but it requires going through enemy territory.
Back at home, Bob and Kim try to expose a man who may be linked to terrorists.
Who you going to call...the team is about to bust a anthrax lab with a leader with field experience but they are being held up by an official who is using high-tech toys to make decisions for him.
Kim's life is in danger when her boss forces her to do something she doesn't want to do.
Jonas and the team trick an arrogant Department of Defense official, who jeopardized a previous mission due to his lack of field experience, into joining them on an assignment so he will observe war up close and personal.
At home, Kim is secretly reunited with her kids.
Jonas plays a game of high stakes no-limit texas hold'em to win back the services of a CIA spy who has gone over to the other side. His success is also the key in getting court martial charges against team member Bridget Sullivan dismissed
Jonas and a seriously wounded Mack take refuge in a monastery where he is ordered to steal the monks' most prized possession.
Back home, Bob is asked to perform a dangerous mission that will reveal the darkest side of his job to Kim.
The President orders the unit to capture a Nazi war criminal from his hiding place and deliver him to The Hague.
In Washington, Tom Ryan confronts his past when he is offered a promotion to General.
As Jonas coaches Betsy before her military-ordered media tour, the Unit initiates a new team member.
Unable to communicate with the outside world, the Unit and their families must survive when a deadly gas poisons anyone in their community who steps outside.
As the Unit fights to rescue Jonas's old friend, a broken helicopter gas tank and nearby guerillas impede their mission.
Tom goes to extreme measures to extract information from a recovering alcoholic whose husband may have been behind a terrorist attack.
The mission's plans go awry and Bob must run interference when Jonas and Mack are undercover to find the terrorists who killed the Vice President.
When Sam attacks Bridget, the other members of the Unit must hunt him down.
A random incident throws Jonas and Bob's carefully planned mission into chaos.
While Jonas is tracking down a Russian terrorist cell, a kidnapped Molly is used as bait.
As you cloud see on the last episode Sam is involved in the kidnapping of Molly. What will happen and how will it finish.
The Unit must locate and diffuse three sets of dirty bombs headed for unknown locations across the United States.
Meanwhile, the team prepares for a wedding of one couple (Charles Grey & Joss Morgan) and the end of a marriage for another (Jonas & Molly Blane) or will Jonas leave The Unit and stay married.