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.

During a maneuver, transposed digits lead to a fatal bombing of a unit's own men. This causes several seriously wounded and eventually one dead soldier. Lt. Rabb and Lt. Austin are assigned to investigate this case because the responsible man is none other than Jay Williams, the son of Gen. Williams. But it seems the case is clear since Jay confesses that this mistake was his fault. Locations: MCB Twenty-Nine Palms

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.

During a test flight Lt. Pendry has a deadly crash with his Tomcat. Harm and Meg are ordered to probe this case and the facts point to a pilot error, not at a system malfunction. Though Pendry was a risk-taking pilot, Harm doesn't think he has gone too far based on his knowledge from his flying days with Pendry. Locations: Miramar Naval Air Station; San Diego/area and off-coast

Cpl. Parr shoots at an intruder, who he believes shot at him first, at the United States Embassy in Lima, Peru. The intruder, an unarmed 15-year-old teen, is killed. But he wasn't just any boy. He was the brother of Cpl. Parr's girlfriend who (according to her) is pregnant. Harm and Meg are tasked to determine if the teenager was, in fact, unarmed, or if this was an attempt to kill the ambassador. Locations: Lima, Peru

Harm and Meg investigate the theft of stolen missiles at the SEATAC Naval Base. While interrogating PO1 Quinn of the theft, a prison-break takes place and Lt. Austin is taken hostage. Contrary to the Major in charge, Lt. Rabb thinks that this is a well-planned breakout with a big goal. Locations: SEATAC Island Naval Base and surrounding areas

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.