The NCIS team uncovers a mole in the ranks while working with the Department of Homeland Security to locate 900 missing pounds of explosives that pose an imminent threat to New Orleans.

When the Coast Guard boards a yacht that is in an area that is used by smugglers, they find the Captain with the crew's waiter who is dead. They try to get him but he resists and kills him. The Coast Guard calls Pride because the yacht belongs to Javier Garcia. Pride thinks Garcia was smuggling something. He calls the FBI to tell them about it and sends LaSalle to help Gregorio. Pride discovers one of the passengers is someone he knows and that she's engaged to Garcia. Instead of arresting the men who took off the yacht what they were bringing in Gregorio decides to follow them instead if arresting them but things don't work out as planned. Isler wants Pride's friend to help them but Pride says it's too dangerous but she agrees to do it.

Unable to trust anyone in New Orleans, the NCIS team calls in FBI Assistant Director Isler (Derek Webster) to help expose and stop the sinister scheme Mayor Hamilton (Steven Weber) has planned for the residents of Clearwater, on the third season finale.