When the NCIS: Los Angeles team and DEA uncover the cartel's plans to slyly transport billions of dollars’ worth of cocaine from Colombia to the U.S. using a submarine, Callen and Sam must quickly locate the missing vessel. Meanwhile, Hetty is called to Washington in the aftermath of the controversial mission in Afghanistan.

Callen and Sam find themselves trapped inside an armed submarine that terrorists are intending to use to hit an aircraft carrier in San Diego. Hetty goes against orders and forgoes her trip to Washington, as the team attempt to locate and save Callen and Sam and stop the terrorist attack.