When a female F-14 Tomcat RIO (Radar Intercept Officer) goes missing from the aircraft carrier U.S.S. Seahawk while stationed in the Adriatic Sea, the Judge Advocate General of the Navy, Rear Admiral Al Brovo (Kevin Dunn), sends young Lieutenant Harmon Rabb with Lieutenant Junior Grade Caitlin Pike on Bastille Day 1995 out to the carrier where they must find out whether her death was accidental or intentional.

Harm & Kate continue to investigate the death of Lt. Angela Arutti, all the while the carrier remaining on combat status.

A civilian tech rep aboard a submarine seizes control of an experimental torpedo after its launch during an exercise. The rep threatens to sink a cruise ship and demands a ransom. Harm and Ltjg. Meg Austin go to the sub and save the day.

Harm and Meg are investigating the death of a Navy officer at the Arlington Cemetery, where during the months before, other Navy officers have been murdered, too. This murder happened after a reception at the French embassy and the trail leads to the Thai ambassador and his wife. Harm is attracted to her as she reminds him of a girlfriend back in Vietnam who was killed. Also, Colonel Patano (the ambassador's guard), is one of the suspects. Locations: Washington D.C.; McLean, Va.; Bethesda, Md.

Cpls. Ednar and Anderson mistakenly cross the Iraqi border. Trying to escape an Iraqi patrol, Cpl. Ednar is killed and Cpl. Anderson is taken prisoner. The Iraqi government invite the United States to send advocates to defend the Marine who's facing the death penalty for espionage. Harm and Meg are assigned to travel to Iraq to act as his lawyers as well as attempt to free the Corporal with the help of an undercover agent called 'Scimitar'.

Meg goes under cover as a Marine recruit in order to investigate the mysterious death of a female private in a boot camp. The facts point at the two drill instructors SSgt. Carrington and Sgt. Gonzales. But a newspaper clipping found by Lt. Austin changes the situation completely. Locations: Parris Island; Washington D.C.

Harmon Rabb is promoted and his first assignment as Lt. Commander is to defend Capt. 'CAG' Boone in a court-martial. During a mission over Bosnia, one aircraft goes down due to a system malfunction. A Serbian helicopter shoots at the parachuting crew and, to protect them, the CAG shoots down the helicopter. Is CAG, indeed, defending the crew from a hostile helicopter, or is he acting out of revenge, violating a cease-fire, and risking a war? Locations: Bosnia; Naples, Italy; USS Seahawk/Adriatic Sea; Washington D.C.

Mac is arrested and placed on trial for a major felony, along with her former commanding officer and mentor, Col. John Farrow. Conviction could result in long prison terms.

Harm volunteers to defend her, but his efforts are thwarted by Farrow's defense attorney, JAG exchange officer, Australian Navy Commander Mic Brumby. Harm feels that neither defendant has come clean with the truth and he begins to search for evidence which is not forthcoming from either one. Ultimately, he learns that Mac and Farrow have each been trying to protect the other. The key witness in the case turns out to be a major surprise to both defendants.