When Harm and Mac are called in to investigate an aborted SEAL operation in Afghanistan, Harm accuses a television news reporter accompanying the SEALs for disobeying orders and causing the error. Meanwhile, Lt. Roberts receives his orders and, leaving Harriet and A.J. behind, ships out for a six-month deployment aboard the USS Seahawk.
After being diagnosed with night blindness, Lt. Cmdr. Harmon Rabb, an F-14 Tomcat fighter pilot, is forced to change careers. Cmdr. Rabb chooses to join the Navy's Judge Advocate General (JAG) Corps. There he both defends and sometimes prosecutes Navy and Marine Corps defendants. He is sometimes assisted by fellow lawyer, Lt. Sarah "Mac" MacKenzie, and his other fellow JAG staff.
Many of Rabb's cases require him to both keep up his F-14 qualifications and travel the world, in order to bring justice to the cases he is trying.
Rabb must also deal with the fact that his father, also a former Navy pilot, never returned home after being held prisoner after he was shot down in North Vietnam. Rabb believing his father is still alive continues the search he has pursued to find his father, since his teens.