After a key witness, Ray, testifies in a federal arms-trading prosecution, he retires as an informant; the team give him a new identity, Charlie, and direct him to a new location; next Callen and company turn their attention to the missing military weapons; however, within two hours Charlie disappears after a shooting in Los Angeles; Deeks goes back undercover while the other members check out the scene. Kensi and Deeks chase around with Ray; a firefight breaks out, and Kensi takes out one shooter, but Ray disappears again; G and Sam seek entertainment and find some, then the gang take Ray's estranged wife to the boathouse, where she talks, where she and Deeks reminisce and catch up with each other, and where Deeks eventually makes a confession; G and Sam make Ray a special deal involving his pregnant honey. During another firestorm the musketeers run a scam on the executioners and therefore on the new convict in a federal prison.

Callen and Sam work with Captain Harmon Rabb, the former JAG, who is now the XO on the USS Allegiance to stop ISIS sympathizers from attacking U.S. aircraft carriers.