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.

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.

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.

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 LtCol Farrow. Harm and Mic clash over defense strategy.

A newspaper prints an op-ed piece, contemptuous of the PotUS (and a violation of the UCMJ), which first appears to have come from Harm's office computer; Harm figures it out. Meanwhile Mac encounters an unusual question about childbearing.

A disabled Tomcat crashes and burns during an emergency landing aboard a carrier. Mac and Mic investigate; they later prosecute Skates, the LSO, for dereliction. Harm defends; while researching he and Bud meet resistance. Justice prevails.

Again at The Wall at Christmas, Harm meets Jenny Lake, a singer who, as a member of a USO troupe, entertained aboard Harm's father's carrier. She tells about their brief friendship. The JAG characters play other roles during flashbacks.

A displeased woman seaman "quits" and walks away; Mac prosecutes, and Harm defends. She argues that her recruiter promised her training and a rating which she has not gotten. Bud makes an announcement, and the admiral makes a date.

Harm and Bud investigate a crash of an F-14 while it leaves a civilian upgrade facility; they find irregularities. Mic, now a civilian lawyer in Washington, represents the vendor. The admiral tries hard to give Sydney a happy birthday.

RAdm. Boone has become nominated to serve as ComSixthFleet and to get his third star. Days before the Senate confirmation hearing, SecNav receives an anonymous hotline tip alleging war crimes in Vietnam by Boone; Harm and Mac investigate.

RAdm. Boone goes on trial for murder of civilians in a village in South Vietnam. Mac and Bud prosecute, and Harm and Loren defend. Webb produces a surprise witness with surprising testimony. Meanwhile RAdm. Chegwidden gets back his SUV.

A Russian nuclear submarine sinks while submerged with a US nuclear submarine nearby. The Russian government learns that the fault for the sinking lies with the Russians, but the officials seek to blame the US anyway. The US submarine leaders know what took place, but they feel reluctant to reveal that, because to do so would disclose an important advantage. After two surprising twists Mac takes a ride aboard a US submarine, and Harm takes one aboard a Russian submarine. The two boats wind up near each other, because the US vessel shadows the Russian one. An extremely dangerous situation develops aboard the Russian boat, and Mac and Harm take part in resolving the problem. Meanwhile a woman ensign in the US Navy graduates with honors in nuclear engineering from a college and from the Naval Nuclear-power School; she then applies but is rejected to attend the Naval Submarine School and to serve aboard a submarine; Mac and Bud advise her.

Representative Latham and another ride an MV-22 Osprey aircraft; just above the sea a minor mishap occurs. Latham holds an inquiry, and Harm and Mac take part. Harriet investigates an old case of innocence. The guys start planning a party.

During a UN peacekeeping campaign a Marine captain, exceeding written rules of engagement, orders his team into an ambush, which kills six Marines. Sturgis prosecutes, and Harm and Bud defend. Mac investigates an unlikely peeping tom.

Harm and Mac go to Saudi Arabia to defend Lieutenant Stephanie Donato, a female naval aviator who flies C-130 Hercules while serving with the U.S. Air Force, but refuses to wear the Abaya when off-base.

Harm and Mac go to sea during wartime operations. Harm flies the next mission, hits the target, and draws enemy fire; his aircraft sustains damage, but he safely returns. Bud runs into trouble at work, and Sturgis becomes closer to Bobbi.

The admiral orders a hearing about the allegedly inadequate defense by Bud in the previous episode. Sturgis prosecutes, and Harm defends. Harm discovers why Bud did not find a key witness and an alibi. The admiral meets an intriguing lady.