During an exercise, friendly fire goes too close to a boat hauling 15 Marines, apparently due to a mistake by PO Mike Roberts, Bud's brother. One by one Bud, Mac, Harm, the admiral, the SecNav, and Webb all fly out. Harm solves the puzzle.

A Russian nuclear submarine sinks while submerged with a US nuclear submarine nearby. The Russian government learns that the fault for the sinking lies with the Russians, but the officials seek to blame the US anyway. The US submarine leaders know what took place, but they feel reluctant to reveal that, because to do so would disclose an important advantage. After two surprising twists Mac takes a ride aboard a US submarine, and Harm takes one aboard a Russian submarine. The two boats wind up near each other, because the US vessel shadows the Russian one. An extremely dangerous situation develops aboard the Russian boat, and Mac and Harm take part in resolving the problem. Meanwhile a woman ensign in the US Navy graduates with honors in nuclear engineering from a college and from the Naval Nuclear-power School; she then applies but is rejected to attend the Naval Submarine School and to serve aboard a submarine; Mac and Bud advise her.

The JAG gang take part in a JAGathon, a charity-benefit marathon, which provides opportunities for personal pride and individual competitiveness. Sturgis feels uncertain, and Harm defends a sailor for impersonating an officer.