Callen and Sam work with Navy Captain Harmon "Harm" Rabb, Jr. (David James Elliott) to locate a group of ISIS sympathizers aboard the USS Allegiance. Also, Hetty enlists her friend, Lieutenant Colonel Sarah "Mac". Mackenzie (Catherine Bell), to help obtain information from a Russian diplomat.

Callen and Sam work with Navy Capt. Harmon Rabb, Jr. to apprehend spies aboard the USS Allegiance. Also, Hetty partners with Marine Lt. Col. Sarah “Mac” Mackenzie to neutralize a missile attack in the Middle East, and Kensi and Deeks are trapped in a mobile CIA unit in Iraq while under attack by ISIS.

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.