While Harm is sent to Russia to help the Russians find a better way to implement their military justice procedures, Mac and Bud remain behind to prosecute a Naval commander charged with selling military secrets to the Russians. Once in Russia, Harm becomes involved in investigating high level corruption in the military.

Meanwhile, Mac is on the verge of making a deal with the traitorous Naval officer when he and his lawyer are murdered. Mac and Webb then discover that the traitor was linked to a Russian assassination plot. But Mac's attempts to alert Harm fail, and he is caught in an ambush with a Russian who reveals the life-changing secret to him.

Harm is distraught when his newly discovered half-brother, Sergei, is framed for a crime punishable by death, while Mac arrives in Russia to prevent a presidential assassination.

When the captain of a U.S. Navy frigate rescues a young girl in Cuban waters and sets off the beginnings of an international incident, Harm and Bud's investigation leads them to Cuba and a meeting with Castro.

When a pretty female petty officer is arrested by the MP's for impersonating a Salvation Army 'bell-ringing' Santa & pocketing the cash, Harm is assigned as her attorney. However, since she has a history of unauthorized absences, she is ordered to be held in custody. But with the holidays, the brig & pre-trial detention center are unavailable, she is estranged from her father, so she must spend the holiday with Harm or with Mac.

Cmdr. Ted Lindsey (as the SecNav's administrative assistant) notifies Bud's brother Mikey that each year, the SecNav nominates 170 enlisted personnel for admission to the Naval Academy and that Mikey is being considered for one of those nomination spots. Bud & Mikey's father, a retired Master Chief though is not at all thrilled with having another son becoming an officer and insures that everyone knows it.

Mac's psychic vision talents come into play when a female Naval officer is found with her throat slashed in a local park. What originally seems like an open and shut case involving a love triangle that led to murder becomes much more when Mac's "visions" show her puzzling images that lead to evidence of an international conspiracy. Together with Sturgis Turner, Mac follows the clues to uncover information that leads them to a possible terrorist plot in Russia to steal nuclear weapons.

Harm defends a Navy SEAL accused of disobeying orders when his return to a hostile area in Afghanistan to retrieve a wounded comrade results in the death of another officer. Complicating the issue is the dead officer's pregnant widow who is determined to have justice served even though the accused man was her husband's best friend. Meanwhile, Admiral Chegwidden is asked to resign when he's charged with slapping a high school student.

Harm faces Mac in court when he defends a Navy medical corpsman accused of murdering a Marine sergeant during a training exercise.

When he finds himself serving on the jury, Bud, feeling like an expert, uses his knowledge of the law during deliberations to help the jurors question the facts of the case, but then discovers the hard way that sometimes things in the courtroom are not what they seem.

Cmdr. Turner goes to New London to assist in the deployment of the submarine USS San Antonio. Once there, he helps a young sailor keep his marriage together when his wife intends to file for divorce due to the deployment.

When its learned that Harm has two tickets to the Super Bowl, everyone in the JAG office jockey for position in an attempt to be selected to go with Harm to the game. However, it turns out the ""tickets"" to the game are not necessarily the best seats for ""watching"" the game.

Tensions run high at JAG when charges of negligence are brought against Bud for not defending his last client effectively. As Harm defends Bud, Sturgis prosecutes and Bud fears that Sturgis has damaging evidence against him. Just when Bud thinks things can't get any worse, Sturgis calls a surprise witness - Mac - who reluctantly takes the stand against her colleague.

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.

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.

A murdered JAG officer teams up the JAG staff with agents of the Naval Criminal Investigative Services (NCIS).

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.