Congresswoman Jenna Flemming is shocked to discover a literal gutless rat in her car, and NCIS takes the threat (which was delivered on a Navy base) seriously. Director Vance takes steps to ensure Flemming's protection while Gibbs and his team, assisted by Clayton Reeves, investigate the threat.

Flemming proves to be rather uncooperative initially, not taking the threat seriously. All that changes when her faithful aide Max turns up dead in a motel pool.

Max's real estate agent girlfriend blames Flemming, stating that the congresswoman had Max on some sort of secret project. It turns out that the project was regarding the potential of Brighton Naval Base back in Flemming's home district in Maryland.

The base's closure would deeply hurt the community of Brighton, and its mayor, Jedd Hamilton, was deeply opposed to the closure. However, he has an alibi.

The team determines that Max's death was accidental, that it was the result of a fight with his girlfriend, who stood to loose a huge real estate commission payday by the base closing. Despite the congresswoman's interference, the team finds evidence proving the girlfriend was with Max around the time of death, and she confesses.

Meanwhile, Quinn worries about Clayton Reeves joining a mysterious and ominous "Operation Willoughby."