Harm and Mac advise students at a naval high-school academy during a mock trial based on an old case in the Navy. The students continue to investigate, and they find a witness not previously interviewed; he gives enlightening testimony.

A court condemned a Marine to death for the murders of three fellow Marines. Mac represents him in his final appeal; Mic represents the USA. Australia recalls Mic, so Harm replaces him. Harm and Mac argue hotly in a new sentence hearing.

Gunny and a Marine buddy stumble into a tussle near a gay bar; the gunny hits another man while helping to defend his friend. A court-martial finds him not guilty, but a civilian prosecutor also puts him on trial. The admiral defends him.

In Korea during the Korean War 23 Koreans died due to gunfire by US soldiers. The civilian press in the USA has refreshed accusations of an unjustified massacre. Harm, Mac, and others fly to Seoul to investigate; a hijacking interferes.

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.

During training five newbies and a jumpmaster jump from an aircraft; the jumpmaster signals the jump too soon; two trainees land in a lake, and one of them sustains an injury and soon dies. Mac and Harm prosecute, and Bud and Loren defend.

A civilian salvage operator announces his intent to claim, seize, and recover the wreckage of a US submarine which the Japanese battle fleet sank on 05 December 1941 while en route to attack Pearl Harbor. The admiral represents the USA.

During an exercise, friendly fire goes too close to a boat hauling 15 Marines, apparently due to a mistake by PO Mike Roberts, Bud's brother. One by one Bud, Mac, Harm, the admiral, the SecNav, and Webb all fly out. Harm solves the puzzle.

Harm goes to Russia to help in reforming Russian military law; however, complications arise. Mac and Bud prosecute a Naval officer for espionage, then she too goes to Moscow. Harriet gets a small surprise, and Harm gets a large one.

A US frigate rescues and takes aboard a 12-year-old Cuban girl clinging to floating debris; internal and international squabbling ensues. Harm and Bud fly out and lend a hand. The girl takes some big steps. Mac and Mic talk more.

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.

Bud feels anger and agony over the recent tragedy in his family; he considers courses of action and makes a decision. Mac moves a ring, and Mic prepares to return to Oz. Webb twice gives Harm news. A secret about Harriet comes to light.

Cdr. Kate Pike briefly passes through the JAG headquarters, the SecNav cancels orders for a rear admiral, and Bud represents an attractive woman Marine corporal who wishes to attend Officer Candidate School, but a tattoo gets in the way.

A Marine sergeant major, on trial for attempted murder, invokes a supernatural event; Bud prosecutes, and Harm defends. A priest from the Vatican investigates the alleged involvement of a chaplain who died during a firefight in Vietnam.

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.

Mic represents a civilian wrongfully jailed in a Navy brig; he settles with Harm and Bud. Gunny goes to New Mexico to pick up a Marine who disappeared after service in the Korean War. The admiral goes fishing and winds up in a firefight.

Terrorists aboard a service boat approach a USN destroyer in a port in the Mideast; a security team stops the boat and finds explosives and a woman Marine sergeant. Harm and Mac investigate. The suspect volunteers for a task for the CIA.

LCdr. Jordi Parker, one of Harm's former girlfriends, dies under suspicious circumstances. For a while NCIS regards Harm as a suspect. Mac, Bud, LCdr. Teresa Coulter, and, later, Harm investigate. The admiral helps Danny to make a choice.

RAdm. Chegwidden holds an engagement party for Mac and Mic. Harm and Mac take part in frank and profound communication amid a parade of incisive and revealing flashbacks. Bud runs into some trouble, and Harriet receives a gift of gold.

Harm misses Mac's rehearsal and dinner by doing his semiannual carquals, then he and Skates eject from an F-14 Tomcat at night during a storm at sea. A rescue helo picks up Skates, but Harm remains unfound in the rough sea. [Continued.]

A rescue helo has picked up Skates, but Harm remains adrift in the sea. With Mac's uncanny help, a Viking finds Harm's life-raft, then a helicopter finds Harm, but his condition is critical. Mac declines to set another date, then Mic returns to Oz.

Mac postpones her wedding indefinitely, and Mic returns to Oz. Mac seeks TAD out of town, so the admiral sends her and Gunny to investigate the disappearance of a Marine major from a ship in the Indian Ocean. Harm heals and gives a ride.

An intruder shoots three Navy people, killing two. One of the dead is a friend of Harm, who protects his reputation. Webb, counter-espionage, and disinformation are involved; Bud solves it. Mac and Renee return to town; Mac leaves again.

A Navy lieutenant ostensibly blows a whistle on an allegedly defective high-tech combat system; Mac helps him to resign, but she discovers his dishonest plot, and she helps justice to prevail. Harm meets a little old lady by accident.