Robert Wagner returns to help NCIS celebrate its 250th episode. When meeting his father at a hotel, Tony sees a man whose uniform doesn't match his rank and tries to question him. The man - Nick Bodeen - runs away, with Tony in chase. Cornered in an alley, the Bodeen points his gun at Tony.
Tony reacts by shooting and killing him. The Attorney General's office puts Tony on administrative assignment while they investigate his action.
Meanwhile, the NCIS team investigates the Bodeen, who was a private detective who was impersonating a Navy officer. They eventually discover that he had just finished killing Senator Denise O'Hara's assistant - Michael Elliot - in one of the hotel rooms.
As it turns out, Bodeen was involved in a bribery scheme with another of the senator's assistants - Jennifer Morrison. Elliot had discovered the plot and had wanted to reveal it, but had been killed by Bodeen before he could do so.
On the family front, Tony's father had shown up with some good news: he is once again engaged. In a comedy of errors, McGee and Bishop observed Tony Sr. entering a hotel suite with a very young and pregnant woman - who they thought was Tony Sr.'s bride-to-be.
It turns out she was his fiance's daughter. Tony and his father eventually straightened out the miscommunication and reconciled.