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.
Two MiGs shoot down Harm and Mac; they eject, and two gypsies befriend them. The admiral follows them to Moscow, then Webb also. After a shootout the good guys help Harm and Mac to continue, and he hears about his father's life and death.
Harm and Mac attend a reception at the Sudanese embassy, where the guard force appears to take over, but Harm and Mac find that the takeover is a scam. Harm puts the word out to the world. A lethal virus turns up, but everything works out.
A Japanese man accuses a US Naval officer of raping his teenage daughter. Harm, Mac, and Bud investigate; a rear admiral applies political pressure. The Japanese conduct a trial, which goes poorly until a witness eventually steps forward.
Harm, Mac, and Bud have gone to Italy for a trial, and the admiral has gone there for an inspection and a visit with his daughter, who becomes abducted. The admiral suspects an involvement with stolen missiles. The JAG team sorts it out.
A former Naval aviator jumps to his death from a high window. Roscoe Martin, a fellow mental patient and a character from a previous episode, faces a charge of second-degree murder. Harm defends him in a court and welcomes him to his home.
Terrorists in the Persian Gulf attack a US Naval warship, killing five sailors. Upon the arrival of one prisoner in the USA, a Marine on a guard detail shoots him. Mac and Bud prosecute for murder, and Harm defends. Surprises abound.
Two F-14 Tomcats encounter two MiGs in a no-fly zone above Iraq, and one of the Tomcats goes down in action; nobody dies. Harm and Mac investigate. The pilot of the surviving Tomcat misses a shot, saying that "a voice" told him not to fire.
A TV-news network airs a report alleging that a Marine team has used sarin gas to assassinate three renegade US civilians working at a plant producing chemical WMDs for Saddam Hussein. Harm advises Rep. Bobbi Latham and her House inquiry.
Mac and a former CO, mentor, and lover go on trial for conspiracy and the murder of her long-estranged husband. Cdr. Ted Lindsey prosecutes, Harm defends Mac, and Mic and Bud defend Mac. Harm and Mic clash over defense strategy.
LCdr. Jack Keeter, a friend of Harm, has unexpectedly landed a stealth spy aircraft in Iran; the Iranian government has announced its intent to prosecute him for espionage. Harm, Mac, and Mic go to Iran, investigate, and intercede.
Chaos rules at the JAG headquarters on Christmas Eve due to a disabling snowstorm, the arrival of a young girl, the admiral's wish to get a substitute flight to Italy, the arrest of a Navy shrink for DUI, and gifts for needy children.