Harm and Mac get separate transfer orders; Harm gets a promotion. Vic investigates and resolves a fraudulent enlistment. Harm and Mac talk, then propose to each other; Bud flips a coin to decide which of them will resign from the service.
Bud has lost his right lower leg due to a mine in Afghanistan; during emergency surgery he faces bad trouble. Sturgis returns to Washington, and Harm and Mac disobey an order from the admiral. Bud encounters an astounding change of course.
Three thugs try to rob a C store, but a homeless former SEAL intervenes and kills them; he runs into a nearby church while Bud prays there. A standoff develops and resolves; Harm successfully defends the SEAL in a civilian criminal court.
Bud and Harriet hold a party on Christmas Eve in their new house for the JAG gang. Everyone runs into difficulties en route, but everything finally works out. Bud invokes, "God bless us everyone"; all agree and exchange, "Merry Christmas".
A Boy Scout finds the decomposing body of Lt. Loren Singer in a tree. The NCIS investigates, and Harm becomes the prime suspect. The NCIS finds not only surprises about the death but also circumstantial evidence pointing straight to Harm.
Harm finds his father's trail in Siberia; he and Mac (who speaks the language) go to Russia. Two Russian acquaintances intercept them. With help Harm and Mac "borrow" a MiG-29 (a copy of the F-14 Tomcat), but opposition suddenly appears.
In south Texas residents have reported strange phenomena, stories of supernatural events have abounded, and a 10-year-old girl has disappeared. Harm and Meg investigate; they find the girl, and they solve the greater mystery.
By mistake a foreign agent sends a fax to Meg's office; then he retrieves it and shoots Meg to prevent her from identifying him. Meg undergoes surgery; Harm and others track and find the assailant, who's an assassin on an assignment.
A car hits Harm; Mac takes him to a hospital, where an Israeli official undergoes a heart transplant. Members of the Hamas seize control of two floors, to hold the official as a hostage for a prisoner exchange. Harm and Mac help.
The season finale finds cast members in a total state of change: Admiral Chegwidden reveals a surprising decision he has made; Mac is given some news about her health and Harm is faced with a personal loss.