Aboard a decommissioned Naval vessel, inspectors discover the skeleton of a missing aviator. Harm and Mac investigate. Harm finds an important book, which contains a clue about the whereabouts of his father, but the book disappears.
A single woman Marine helo pilot, an officer, faces charges for disobedience and an adulterous relationship with a married enlisted man. Mac and Bud prosecute, and Harm defends. Rep. Bobbi Latham attends, to ensure equal treatment.
A Marine recon team extracts other Marines imprisoned in Haiti due to rebel action; civilian deaths result. The officer in tactical command stands accused of disobeying an order to wait. Harm and Mac prosecute; the admiral and Bud defend.
An F-14 Tomcat clips the top of a utility tower. The aviators eject, but the aircraft crashes and kills two people on the ground. The evidence implicates the squadron CO, a mentor of Harm, who investigates and prosecutes. Mac defends.
A paraplegic Marine veteran kills a Vietnamese man in Georgetown, then he goes to the JAG headquarters and confesses. The victim was the cruel commandant of the vet's PoW camp. Harm volunteers to represent the vet in the civilian court.
Inside the Bermuda triangle an armed F-14 Tomcat vanishes. The pilot's wife and daughter suddenly disappear from family housing at NAS Jax. Harm, Mac, Bud, and even the admiral investigate; they figure it out, and the Navy makes it right.
A carrier-based F/A-18 Hornet accidentally fires a missile and destroys an aircraft first described as a North Korean commercial liner. Harm, Mac, and Bud investigate; they discover not only the cause but also a spy message and the spy.
A SEAL team rescues a captive US diplomat in Lebanon; the PotUS wants the OiC of the team to receive the Medal of Honor. Harm, Mac, and Bud investigate, but they have trouble in learning anything because nobody talks; Harm figures it out.
A Marine Corps helo has a midair collision with an unknown aircraft; all but the pilot survive. Harm and Bud investigate. People from a mysterious agency take control of the site, and Harm locks horns with them, but he solves the mystery.
Harm tries to buy stolen documents allegedly about his father in Russia, then Harm faces a charge of murder. Webb helps Harm. The matter goes to a pretrial hearing; Mac represents Harm. Afterward Mac suddenly again speaks with the admiral.
A woman Navy ensign shoots and kills a Turkish colonel; she claims self-defense. Harm, Mac, and Bud investigate, and Harm defends her in a preliminary hearing. Later the admiral tells Harm more. Bud and Harriet take another step together.
Annie Pendry and her son, Josh, have moved to Baltimore. During a field trip Josh watches a murder; Annie seeks help from Harm, who obliges. Josh experiences gunfire, a kidnap, and intimidation. Harm, Mac, and the admiral rescue Josh.
An admiral, a friend of A.J., dies, apparently by suicide; then someone stabs another admiral to death. A.J. refuses to accept the finding of suicide; he, with help from Harm, Mac, Bud, and Harriet, connects the dots. He's the next target.
A Marine corporal, driving a tank, accidentally demolishes a tent; he then faces a court-martial. His domestic life has diluted his attention. Harm, Mac, Bud, and Dalton all work to defend him and to represent him in a custody contest.
A Navy frigate fires two warning shots across the bow of a suspect yacht, which has refused to stop when ordered; the second round appears to hit the boat, and it sinks. Harm, Mac, and Bud investigate; they figure out what had happened.
An enlisted woman at sea makes a serious mistake; no casualty results. The command master CPO calls her to his office for counseling; she then accuses him of unlawful sexual behavior. Harm and Bud prosecute, and Dalton and Harriet defend.
Dalton tries to reconcile, but Mac says no; he seeks one last meeting, then he dies in her arms. Harm and Mac defend a CPO. A stalker captures Mac, but Harm frees her. The admiral introduces his daughter; Bud and Harriet still have trouble.
Harm, Bud, and Josh take part in a tiger cruise; the ship's crew "rescues" people from a raft. The newcomers are anti-Castro terrorists who seize the ship and launch missiles to hit Castro. Harm and Josh work together to help defeat them.
Mac learns more about Ltjg. Diane Schonke, who (in season 1) looked so much like her. While Harm reexamines an old cache of letters, he deduces who killed Diane. Harm intercepts his suspect; Mac arrives, and the killer takes extreme action.
Palmer captures Harm and makes a mask of his face, so that he can impersonate him. Palmer, the imitation Harm, goes to a hearing, where he tries to kill a Marine officer accused of violating a weapons treaty. Bud gives Harriet some jewelry.
The Marine Corps returns the remains of a WW2 codetalker to a Navajo cemetery, but a native medicine woman denies that the remains are his. Harm, Mac, Bud, and Harriet investigate. Truth emerges, and Harm proposes an acceptable compromise.
In Italy an F-14D Tomcat has a midair collision with a civilian helo; six locals die. The Italian government wishes to prosecute the Navy pilot for manslaughter. Mac prosecutes; Harm and Bud defend and persist, and the truth becomes known.
Bud Sr. and Mike (Bud's father and younger brother) travel to Washington for Bud and Harriet's wedding. Bud Sr. leaves insults, injuries, and hurt feelings in his wake; Harriet's mother also causes much discomfort and embarrassment. Bud passes a big career milestone with grace and empathy. A dry cleaner loses Harm's dress whites, but Harm finds them in an unusual place. The girls go to Harriet's party, then Mac bails Harm, Bud, and the admiral out of a DC jail after Bud's party. Bud Sr. skips the beautiful wedding, and Mike arrives late. Harm takes charge of a detail ...
Harm finds his father's trail in Siberia; he and Mac (who speaks the language) go to Russia. Two Russian acquaintances intercept them. With help Harm and Mac "borrow" a MiG-29 (a copy of the F-14 Tomcat), but opposition suddenly appears.