The Unit is a covert team of U.S. Special Forces operatives who must undertake missions around the world. The latest newcomer is Bob Brown who joins Jonas' team and they set out to rescue an airliner filled with European businessmen who have been hijacked by terrorists. Meanwhile, Bob's wife Kim is struggling with how much control the Unit has on her own personal life.

Jonas attempts to rescue a group of American missionaries in hiding in Indonesia. However, he soon realizes the mission is going to take more manpower then he expected. At the base, Mac ends up being shot by Bob during a training exercise and Molly, Kim and Tiffy prepare to host a visiting senator.

Jonas and his team must track down surface-to-air missles before they are smuggled out of Brazil after a deal with a drug lord falls through. Jonas gets help from a local boy who informs the team where the SAMs have been taken to be shipped. Meanwhile back on the base, Kim ends up causing even more trouble when she insists that the “Family Readiness Group” deals with what she deems more serious issues. Also, Williams tries to find a way to tell the woman he wants to marry that he is actually a Unit member and not a clerk on the base like she believes.

The Unit is sent to Los Angeles to protect Mexico's drug minister who has been threatened with assassination and soon his wife and sons are kidnapped. At the base, a former Unit wife makes a return appearance in the hopes of luring the Unit members away. Tiffy is upset when Ryan orders Mack to take time off.

Jonas and the team carry out an assasination of a terrorist in Spain. However, they soon find out that the government called off the mission and will now not protect them in the country which means there only hope is to escape. Back at the base, Molly learns that her daughter Betsy wants to drop out of college and Kim thinks about taking a college course herself.

The crew must fly to Afghanistan to assassinate a high ranking member of the Taliban. However, one of their team helicopters ends up going down in enemy territory, placing the entire crew in jeopardy. Back at the base, Molly confronts a friend and retired Unit veteran about his addiction to painkillers and Kim ends up getting a job at the local radio station.

The team travels to Iraq to save Jonas' daughter, who has been kidnapped; Col. Ryan must face the consequences for his adultery with Mack'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.

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.

When several dirty bombs are found on American soil, The Unit is deployed to find and diffuse. On the home front, the wives prepare for a wedding and a possible divorce.

The team keeps trying to rescue Betsy Blane from Syrian captors; Mack has an opportunity to get revenge on Ryan for his affair with Tiffy.

Molly is kidnapped and used as bait, while Jonas is out of the country looking into a Russian terrorist cell.

The team follows a scientist who may have been targeted by terrorists, hoping to link those same terrorists to a presidential assassination plot.

A random incident throws Jonas and Bob's carefully planned mission into chaos.

Hoping to con a terrorist into exposing his accomplices before they escape, the team produces phony evidence of an attack.

Jonas and the team force a Department of Defense official to go with them on an assignment and experience the realities of war; A mysterious women shows up at Aerodyne headquarters. Kim is finally reunited with her kids.

The unit initiates a new team member while Jonas coaches his daughter Betsy, on how to respond to media questions about her kidnapping and rescue without blowing the cover story.

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 nuclear scientist insists on making a deal with the team before revealing information about an imminent terrorist attack on a major U.S. city; Kim, Molly and Tiffy are asked to work under cover with Jonas.

The team's attempts to raid an anthrax lab are thwarted by an official from the Department of Defense (Michael McKean), who believes his high-tech intelligence is superior to field logic.

Jonas plays a game of high stakes baccarat to win back the services of a CIA spy who has gone over to the other side. His success is also key in getting court martial charges against team member Bridget Sullivan dismissed.

The team, minus Bob, are in search of a fallen Chinese satellite. This quickly turns into an opportunity to capture one of the world's most wanted terrorists. Meanwhile, Bob is questioned about the Unit's role in the rescue of the hijacked plane. Molly decides to visit the Unit's psychiatrist about the shooting at her home. Kim is frustrating about moving and then comforts a woman who has just learned her husband has died in combat.

While the Unit is investigating a man they believe to be smuggling nuclear weapons, they discover that he is also smuggling women.

Bob and Mac both find themselves in trouble when they each take assignments undercover. Bob as a chemist who hides cocaine by converting it to paint and Mac as a fighter trying to bust an illegal betting ring.