Three recurring characters are also introduced: the main foe for the first two seasons, Ari Haswari; Special Agent Timothy McGee and Jimmy Palmer who replaces Gerald Jackson, Ducky's assistant, after he was shot.

But while his death is originally thought to be a tragic accident, NCIS eventually uncovers evidence suggesting the commander was in fact murdered and that it might be connected to a possible assassination attempt on the President.

Tony, Abby, and McGee are tasked with identifying the deceased, while Gibbs and Kate are sent underwater on a submarine to vet five possible suspects, one of whom might have been responsible for the murder and to also prevent a possible sarin attack from taking place.

As Ducky meets his new assistant, Jimmy Palmer who is replacing the injured Gerald Jackson, Gibbs and the team handle the case of a marine found impaled on a tree stump after being shot with a SMAW.

Working with ATF Special Agent Stone (Bellamy Young), Gibbs poses as a weapons supplier to complete the deal, and must double-cross everyone in order to find the corrupt person at the center of the investigation, and the one responsible for the marine's death.