Harm is sent to Washington, D.C., to join a committee formed to judge the validity of a shocking television report -- that U.S. forces used sarin gas on fellow Americans during the Gulf War. What he uncovers, though, is so unexpected that he can't present it without testimony from a key witness, Sgt. Morrison, who was actually on the mission in question in the Gulf, but has been missing ever since.

Meanwhile, Mac is caught off guard when an old flame, Christopher Ragle suddenly reappears in her life.

Harm and Mac's original mission is to represent a Navy flier whose Stealth jet is thought to have crashed in Iran due to a mechanical failure. But when the pilot slips Harm a message indicating that the $80 million plane didn't crash and is hidden, the assignment becomes nearly impossible: get the pilot -- and the costly aircraft -- back to the U.S. without letting the Iranians know that the plane is intact.

Admiral Chegwidden and Clayton Webb make an unlikely team when they join forces to save a C.I.A. agent from Italian terrorists. Webb already tried once unsuccessfully to liberate the C.I.A. agent, who was his mentor, and knows he needs backup in order to retry the mission. He approaches the Admiral, with whom he has a tenuous relationship, but who he knows credits the agent with saving his life in Vietnam. Together, Webb and Chegwidden go to Italy and put into motion a dangerous trap for the terrorists that, if it backfires, will kill all involved. Meanwhile, Harm suffers an identity crisis when his classic Corvette is stolen.

As Harm considers his future at JAG, he learns that Charlie Lynch -- the ex-Navyman responsible for the murder of Annie, the abused child whose death still haunts Harm -- has resurfaced, placing the little girl's twin sister, Dar-lin, in danger. Putting his career decision on hold until he closes the chapter on Lynch, Harm tracks him to a shipyard where the vicious killer is holding Dar-lin hostage. Overflowing with anger against all Lynch's grisly acts of murder, Harm finds himself in an intense stand-off with him that will leave only one man standing.

Unexpectedly, the wily Buxton demands that Harm and Brumby be his lawyers, thereby preventing Harm from testifying against him and forcing the two adversarial lawyers to work together. The contentious trial continues with Mac and Roberts prosecuting, and the pressure is enormous as the U.S. Navy and the Russian government vigilantly follow the trial to ensure that its own agendas are met. Meanwhile, the Navy has its own special plans for the troublesome Buxton.

Harm faces a court-martial when a letter critical of the President appears on the Op-Ed page of a newspaper and is traced to his computer.

As an investigation threatens Harm's promotion as well as his entire career, a well-known conservative organization offers to represent him and Harm accepts. The key to Harm's defense is to find the actual letter-writer, so Bud digs through Harm's old case files searching for those with an axe to grind.

Harm is trapped below deck on a sinking ship with a sailer, who has been accused of murder, and a guard. Some rescue equipment collapses, blocking the only escape route. As water begins to fill the room, the three men are certain that the situation is hopeless.

At the request of Lt. Cmdr. Brumby, Admiral Chegwidden sends Harm and Bud to Australia to represent a U.S. Naval officer, Kevin Lee, who has suddenly surfaced 28 years after being "murdered" by an Australian sailor. Lee contends that he accidentally killed his Australian nemesis years ago and, in a panic, exchanged identities with the dead man.

Now, charged with both deserting and murder, Lee is to be tried in an Australian court, pitting Harm against Brumby. Harm and Brumby are also about to go head-to-head outside the courtroom when Mac appears in Sydney and Brumby decides it's time to make her choose between him and Harm.

The murder/desertion trial of Kevin Lee takes a bad turn after his wife changes her testimony under cross examination.

Harm and Mic fights to win over Mac

Bud's underachieving brother is accused of making a mistake during a training exercise that nearly killed 15 Marines. But establishing his innocence proves to be a difficult task, thanks to the age-old tension between the Navy and the Marines.

Adm. Chegwidden frets over a speech he must give when he is to be given an award.

Mic Brumby returns unexpectantly to the States; Mac & everyone are stunned when he announces that he has resigned his Royal Australian Navy commission so that he could move to the USA and be by the "woman he loves."

Adm. Boone (CAG aboard the USS Seahawk, ""A New Life"" & ""Chains of Command"")is nominated to become the Sixth Fleet Commander. An anonymous informant accuses Adm. Boone of massacrering civilians during the Vietnam War, and Harm and Mac are given only four days to investigate the claim, in part one of a two-part episode.

When Gunny goes to New Mexico to bring back a Korean War hero accused of desertion, he is ambushed by people trying to kill the man.

As Bud is defending his brother Mikey, a petty officer accused of murdering a Mexican in a barrom brawl, their father shows up.

In 1944, in the midst of World War II, a disastrous explosion rocked the U.S. Navy's Port Chicago near San Francisco, killing more than 350 sailors, most of them African-Americans. Following the blast, a group of 50 sailors refused to return to work until changes were made to assure their safety. They were charged with mutiny and court martialed, but later their convictions were reversed. Now, a surviving sailor wants his record and those of all the other ""mutineers"" cleared. Asked to handle the investigation discreetly, Cmdr. Turner discovers that an injustice was done and goes head-to-head with Lt. Singer in the courtroom. Meanwhile, Harm goes house shopping with Lt. Sims.

Harm, Mac & the Admiral return to the office from the USS Seahawk after finishing up with the military tribunal. The office staff is very happy to see the Admiral back in charge, after having to deal with Lt. Singer while he was gone, with Harriet making sure the Admiral knows how ""happy"" they are.

Their joy is short-lived however, when they learn that respected Navy JAG Judge, Captain Sebring is charged with having causing an another vehicle off the road which injured the female driver & killing her 6-month old daughter. Harm is given the task of defending him, while Mac is ordered into the uncomfortable position of prosecuting him. Seeing Mac's dilemma, Cmdr. Turner offers to sit second-chair with her, so that she won't be alone.

Lt. Singer overhears Harm & Mac discussing Bud & Harriet and learns that Bud doesn't know Harriet has bought a house, while Bud hasn't told Harriet about PO Coates.

The episode starts with a short recap of where we left off last season: Bud & PO Coates walking along a dirt road enroute to attend the ground-breaking of the new school, when they spot a small boy playing in a field that had yet to be cleared of mines. As Coates runs for help, there is an explosion behind her. She turns in time to see Bud injured in the explosion and runs to his side. Coates insists that Bud must be transported on the helo that brought them in, that Bud won't be able to wait for the proper medevac chopper.

Bud is airlifted to a field hospital, critical, but still alive. As luck would have it, ZNN reporter Stuart Dunston just happens to be at the base camp when Bud is brought it. Dunston reports the arrival of an injured JAG officer that was brought it, but does not report the name. Chegwiggen advises Harriet, but reminds her he is still on the Seahawk. She tries to contact him by instant messaging, but does not receive a reply.

Harm returns to Washington, DC and is shocked to discover that Admiral Chegwidden had actually processed his resignation through official channels. Also, a female petty officer listed as missing in action during Desert Storm is located in Iraq, married to a bedouin sheik. As a result, the Navy charges her with desertion.

Cmdr. Turner defends himself against the complaint filed against him for displaying anti-Korean attitudes when assigned to deal with the SARS outbreak earlier.

Harm & Mac go up against one another in the case of a Marine General making public speeches stating Islam goes hand-in-hand with evil & terrorism.