Nick Torres and a Metro PD Detective, Higgins, are on a stakeout waiting for a suspect to arrive so they can arrest him. During the arrest, Higgins vanishes without a trace.
Video evidence reveals that he apparently left of his own accord with a woman, shown by fingerprints to be another Metro PD Detective, Lane, who was supposedly killed in an explosion ten years earlier.
The team, along with Detective Sergeant Sportelli from Metro, begin the search and eventually locate Higgins, who is unfortunately deceased from a gunshot wound.
They learn that Detective Lane had been investigating a mobster named Benjamin Sitano at the time of the explosion, and that a million dollars in bearer bonds went missing.
Sinato's son, Benny, denies having anything do with Lane or Higgins and claims to have gone legitimate.
The team finds Lane and brings her in. She claims to have never had the bearer bonds. She became pregnant while undercover, and Benny was the father. She thought there was a mole in the department when the explosion occurred, and that it was meant for her.
After Lane's son is kidnapped, the time checks out Benny's bodyguard, Nitro, an ex-cop who claims that his former boss -- none other than Sportelli -- is crooked.
They track down Sportelli, who commits suicide rather than face the music.
Meanwhile, Ducky is lecturing in Edinburgh and is approached by a friend from New York who wants him to guest lecture for a semester at John Jay, plus write a definitive book on forensic pathology.
After giving the request some thought (as well as consulting a supportive Gibbs), Ducky decides to take her up on the offer, as Jimmy is more than capable of handling things at NCIS without him.