Webb convinces Harm and Mac to go to a dinner at the Sudanese embassy in Washington. The embassy soon becomes under siege by a faction in the Sudanese government. Harm and Mac try to find a way out and discover the real reason Webb wanted them there; they find a cache of a lethal virus in the embassy. The Admiral won't let Webb leave the JAG headquarters until Harm and Mac are out of the embassy.
JAG heads to Italy to investigate illegal arms sales. While the Admiral spends time with his daughter, she's kidnapped. They suspect her abduction is connected with the arms sales. Rabb and Chegwidden go after her.
A marine assigned to a protection detail turns around and shoots the suspect, it's caught on film. Mac prosecutes, and Harm defends. Later a private citizen hires a lawyer for the Marine. Mac finds herself facing off against her former law professor.
A pair of aviators patrolling a no-fly zone encounter some MIGs. In the ensuing dog fight, one pilot gets a lock on a MIG but fails to fire. The pilot claims to have heard an order not to fire. JAG investigates.
A reporter writes an article criticizing the military for using nerve gas on a mission. Congress organizes a committee to investigate. Harm is assigned to the committee as an advisor. Mic Brumby joins JAG on a TAD from Australia. Mac's ex-husband comes for a visit.
A snowstorm hits on Christmas Eve Day while Admiral Chegwidden tries to find a flight to Italy. A girl claiming to be Mac's daughter shows up at JAG. Mac tries to help find a place for the girl to live. In the meantime, Harm meets a navy psychiatrist accused of driving under the influence.
After a night on the town with her shipmates, a sailor is assaulted. Her shipmates get revenge for her by attacking the civilian they think is responsible. JAG must prosecute the crew for assaulting the civilian.
While the Admiral takes some time off, he consults on a script. Harm is in charge at JAG. Mac and Bud defend an officer against charges when he and his men fail to take an earlier flight with civilian causalities resulting from his delay.
While on a training mission in the mountains, a Navy seal comes under fire from an apparent deer hunter. When he returns fire, he finds the body of a young boy. He is soon put on trial by a militia for the boy's death. JAG investigates
Harm starts getting calls from his father. And tries to determine if it really is his father or someone is playing games with him. Meanwhile the Admiral prepares to argue a case before the Supreme Court, the staff helps him prepare.
Webb's mentor is kidnapped, and held for ransom in Italy. He goes to Chegwidden for help. The victim was A.J.'s spotter/friend when he was a SEAL. The Admiral and Webb must work together to save their mutual friend. Bud and Harriett search for family vehicle. Harm also searches for a new car.