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.