A Marine thought to be dead is left behind on a mission that involved kidnapping a drug lord in Columbia. The target of the mission, Estruga, claims that the Marine is injured badly, but still clinging to life. The JAG team, who are already in Columbia to look into the passing of the Marine, agrees to a meeting with Estruga. However, the meeting results in the kidnapping of Webb.
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.