Gibbs is enjoying his morning cup of coffee when he spots a familiar face outside the cafe. Without waiting for his takeaway cup, he immediately leaves and follows after a man.
When he doesn't show up for work, the rest of the team quickly becomes worried. They investigate and soon discover Gibbs's abandoned vehicle and discover his cell phone, credentials, and other identifying items in a mailbox.
Using nearby cameras, they discover that he rendezvoused with Bodie Whitman, who was connected with one of his last undercover assignments. Bodie's brother Ramsay was placed on the most-wanted list after the theft of some nuclear rods.
The team manages to track down Gibbs and Bodie and give Gibbs both his undercover wallet and a wire so they can listen in on them. Gibbs, playing his previous role of anti-government militia type Leland Spears, asks Bodie to put him in touch with Ramsay.
Unfortunately, Ramsay somehow learns that "Leland" is actually a federal agent and tells Bodie. Gibbs is forced to kill Bodie in the ensuing standoff.
Bodie is revealed to have been suffering from Huntington's disease. Given the hereditary nature of the disease, it is likely that Ramsay also suffers from it. The team uses that, along with cell phone data, to track down Ramsay.
Ramsay easily surrenders instead of fighting, and willingly signs both a confession and gives up his mole in the government, who was working for the Department of Energy.
Meanwhile, Bishop (with covert help from Reeves) continues an under-the-table investigation to locate Chen, the man who was responsible for the death of her boyfriend, Qasim.