Callen and Sam travel to the USS Allegiance in the Persian Gulf to work with Navy Captain Harmon "Harm" Rabb, Jr. (David James Elliott) when the NCIS team uncovers ISIS sympathizers who are targeting military locations.

While Callen and Sam are aboard the USS Allegiance, the ship is placed under quarantine for possible Ebola exposure. Also, Kensi and Deeks investigate the murder of a petty officer who recently departed the USS Allegiance and is linked to the Ebola exposure.