A Navy lieutenant on shore leave becomes dizzy and sick while visiting a bar. He wanders outside and is struck by a taxi.
Doctor Wade and her staff determines he was infected with bubonic plague.
The NCIS team contacts Director Vance, who sends Agent Tony DiNozzo down to New Orleans to help the team contain any outbreak.
They attempt to get in contact with all of the sailors on shore leave, to make sure they aren't infected, and to prevent them from infecting others.
Meanwhile, Pride, Tony and the ship's captain attempt to locate the place where the plague began. Usually it's carried by a flea or rodent.
In one of the ship's quarters they find another sailor, dead from the plague. They find a mouse too, but it turns out he's healthy and wasn't carrying the plague.
The lab scientists, along with Abby, determine that the plague sample they have was synthesized - it wasn't developed naturally. Someone had deliberately infected the Navy seamen.
They discover that a couple of the muffins consumed on board had been spiked with the disease.
Pride and the team go over the ship's roster and discover that there was one visitor to the ship - a pharmaceutical company owner, Doctor Mitchell Hufcutt. They realize he had a vested interest in spreading the infection, as his company could provide the antidote and vaccine.
Upon learning that he was on his way to a doctor's convention, ostensibly to infect them so that he could sell them his cure, they located him via GPS. Pride struggled with him, and threatened to throw him into the canal. As the doctor couldn't swim, he panicked and confessed to having more of the plague with him.