The first season of The Unit was originally broadcast between March 7, 2006 and May 16, 2006, it introduces the members of The Unit and their families. As the season progresses various plots and story arcs are explored, such as Tiffy Gerhardt's affair with Colonel Tom Ryan and Molly Blane's mission to find the army widow who conned her out of her savings. In the United States, the first season of The Unit averaged 15.5 million viewers and was the fourteenth most watched show during the 2005–2006 television season.
In the series premiere, newcomer Bob Brown joins Jonas' team as they set out to rescue a hijacked plane filled with European businessmen.
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.
Jonas attempts to rescue a group of American missionaries in hiding in The Philippines, but the mission becomes more complicated than he expected when two members of the missionary group refuse to leave.
When Alberto Salazar, the new Mexican drug minister, arrives in Los Angeles for high-level discussions with the DEA, the Unit has reliable intelligence that a Mexican cartel plans to assassinate him.
The Unit is disavowed by the Spanish government and its members become personae non gratae after they successfully carry out an assassination on their latest mission in Spain.
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
A joint mission to intercept the Taliban leader's convoy in Afghanistan is disrupted when Bravo team's helicopter goes down with engine trouble.
Based on the real-life training course that the military uses to prepare for capture by enemy forces, the Unit takes on SERE (Survival, Evasion, Resistance, Escape), a grueling training exercise of torture.
After an effort to buy surface-to-air missiles (SAMs) 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.
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 Keith Soto, 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.
The Unit is called in to consult on a bomb planted in an Atlanta bank, but they must take control when they learn that the bomb might be nuclear.
Despite encountering several obstacles, the Unit detains a former Yugoslav general wanted for war crimes and lets the UN take credit for the capture. However, unbeknownst to the team, the criminal escapes.