Bud fights for his life after having his leg blown off by a land mine and being operated upon multiple times. Admiral Chegwidden and Lt. Singer testify before the Senate Intelligence Committee about their roles in the search for Kabir Atef.

Mac and Harm defend a Marine corporal (Steve Petrarca) who’s charged with desertion. He claims that anti-Semitism drove him to leave the Corps and join the Israeli army, where he was awarded for heroism.

Harm defends a Marine gunnery sergeant who killed his wife, but claims it was self defense while he refuses to let his son testify on his behalf. Meanwhile, the JAG team bids farewell to Lt. Singer who is departing for the USS Seahawk.

Harm prosecutes a sensitive case in an episode that sees the swearing in of a new Secretary of the Navy and the arrival of a new JAG Officer. Shortly after assuming his new role, SecNav Sheffield appoints Lt. Cdr. Tracy Manetti, a Harvard Law grad, to Adm. Chegwidden’s team. Her first assignment is second chair to Harm in a negligent-homicide case against Lt. Reynolds, a SEAL. While leading a guerrilla wargame among civilians in rural Virginia as a test of unconventional warfare, Reynolds failed to stop for local police, leading to a high-speed chase in which a deputy was killed.

Harm is ordered to defend a plane-maintenance officer who he believes is guilty of making an error that caused the death of an aviator. Meanwhile, Harriet unintentionally impedes Bud’s rehab when she insists he rest at home.

Harm defends a female pilot accused of sexual harassment by a member of her crew who claims she ruined his future in the military because he rebuffed her advances. Harm is skeptical of his client’s denials of the charges, while his co-counsel, Lt. Cmdr. Manetti, is sympathetic, causing tension between the JAG lawyers. Prosecutors Mac and Sturgis seem to have an open and shut case with their star witness testifying until Harm throws them a curveball that throws the case wide open.

Harm, Mac and Turner go up against the CIA’s top counsel when the agency tries to keep a 1968 Navy sub tragedy, in which 129 men died, classified. In so doing, they must find a way around the CIA’s classified information rules in order to follow the orders of the new Secretary of the Navy.

Harm doesn’t have much hope in his defense of a two-star general court-martialed for disobedience and reckless endangerment during a wargame. His job is made more complicated when, in a rare move, Mac is appointed as the judge.

The futures of seven seamen hang in the balance due to Lt. Singer’s recommendation of court martial for all of them following a mishap on the ship. However, Singer’s career could also be doomed if the father of her unborn child is someone on the Seahawk, and it’s Harm and Mac’s job to find out who it is. The problem is, the career-oriented Singer isn’t talking, so Harm enlists the help of Lt. Manetti to do some sneaky behind-the-scenes investigating in order discover the identity of the father.

Harm and Mac investigate a Marine general’s claim that a Navy doctor caused the death of his teenage daughter during routine surgery. Meanwhile, Bud is so frustrated with the simple cases he’s been given that he decides to investigate what appears to be an open-and-shut case and gets surprising results.

This episode pays tribute to the Navy nurses who served during WWII. In the best tradition of "Ghosts of Christmas Past" which paid tribute to the USO entertainers past & present; "Overdue & Presumed Lost" which saluted the sailors who have been a part of the submarine community, running deep & running silent on their 100th anniversary, "Each Of Us Angels" continues that great tradition by focusing almost exclusively onboard the Navy hospital ship, USS Goodwill, during the battle of Iwo Jima in World War II.

In yet another "ripped from the headlines" episode, Harm takes his turn on the bench in a ’friendly fire’ incident, whereby British troops were killed after an American pilot accidentally dropped his bomb ordnance on their location. Mac is assigned to prosecute the pilot, but has to deal with Harm’s repeated impartial rulings. Harm though has his own problems as the SecNav makes it crystal clear to him that a conviction is required to satisfy the British. News reporter Bill O’Reilly is featured.

When Harm takes Admiral Chegwidden for a ride in a F-14 Tomcat, AJ must fight for survival after accidentally being ejected into a heavily forested area, blanketed in a snowstorm.

Cdr. Turner gets to hitch a ride on a submarine that is bound for the mideast when it has been discovered that a 10-kiloton nuclear warhead has turned up missing.

While Harm and Sturgis deal with a Vietnamese smuggling operation, JAG HQ must deal with Commander Lindsey conducting an audit of JAG operations.

Having felt betrayed in the past by the present members of JAG, Commander Lindsey delivers his report to the SecNav critical of the Admiral & the rest of the staff at JAG. After ZNN reporter Stuart Dunston reports on a heroic Petty Officer named Steven Wilson, a woman who sees him on television claims that he is an imposter and that the real Steven Wilson died on 9-11.

When a JAG officer is murdered, NCIS is called in to investigate the death.

NCIS Agent Gibbs continues his investigation on the terrorist, Amad Bin Atwa to avert another attack on a Navy ship. Harm is court-martialed for the murder of Lt. Singer.

A year ago, Sturgis was assigned to prosecute Bud against charges that Bud was derelict in his duties while representing his client in court. Now, Sturgis competency in handling a case is questioned and Sturgis must now rely on Bud to successfully defend him. When the CIA learns that a drug lord is attempting to sell missiles to terrorists, Clayton Webb (re-assigned to South America in "Need to Know") is assigned to prevent the deal from going through. To help with his cover, Mac is sent from Washington to masquerade as Webb’s pregnant wife.

In Paraguay, Mac & Webb continue their mission to thwart the drug lords & terrorists. Harm continues to deal with his emotions where Mac is concerned. Worried about her, Harm turns to CIA Attorney Catherine Gale for help in determining Mac’s location. However, Harm ends up helping Ms. Gale with a personal issue of her own.