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.

When Fatima is captured while on a mission and held for ransom, Callen and Sam enlist a deep undercover CIA agent, Kadri, to help get her back.

Sam, Callen and Rountree travel to Afghanistan when Marine Lieutenant Colonel Sarah "Mac" MacKenzie asks NCIS to help with a sensitive case after two SEALs claim their chief murdered an unarmed prisoner.

When a Russian bomber goes missing while flying over U.S. soil, Callen and Sam must track it down in the desert and secure its weapons and intel before the Russians on board destroy the plane. Meanwhile, Hetty gives Nell a cryptic assignment.