On this episode of NCIS, there's a joint Coast Guard and NCIS training exercise at sea. During the exercise, Gibbs and CGIS Agent Borin spot a deceased man overboard.
He is later discovered to be a missing crew member from a ship named the San Dominick - which is 60 nautical miles away from where the body is found.
At first they believe the dead man to be Joe Willis, who was hired to be a security guard for the ship. But after forensic analysis, Abby identifies him as Ernesto Vilandro, a man wanted in five countries for piracy.
Joe Willis had been killed and submerged in his bathtub for about a week while hijackers had taken over his home, preparing to hijack the San Dominick. Vilandro had posed as Willis by using his credentials, and had then boarded the ship.
Gibbs orders Bishop to return to NCIS with the dead man while he and Tony pursue the San Dominick, which has been out of communication and off course from their original intended destination.
While Borin and Gibbs question the captain of the San Dominick, he collapses, and Gibbs discovers that he's been a victim of a stabbing.
After sending the captain off to hospital via medical chopper, they investigate the ship's radio room, where they see signs of violence, including a destroyed radio.
Gibbs also discovers a piece of paper in the radio room with a set of numbers on it. This number is sent to Abby so she can find out what it means.
NCIS determines that one of the ship's crew - an engineer named Renaldo Aranda - is one of the pirates too. As Tony relays this information via radio to Gibbs, Aranda shows up with a gun to the head of a Petty Officer, and tells Gibbs to stand down.
Aranda tells Tony his demands for keeping the hostages safe: he wants Tony to bring him $10 million dollars.
The captain tells Tony that the pirate crew posed as his crew and boarded the ship. He said he recognized Vilandro from a time before when he encountered him during a hijack situation. He further explained that he fought Vilandro, busted up the communications equipment and threw him off of the boat, thereby killing him.
Arando decides NCIS isn't being cooperative, so he decides he's going to kill one of the hostages. Gibbs offers himself up as the hostage to be killed and Arando agrees.
Abby discovers that the numbers found by Gibbs identify a shipping contained, owned by LCD Liquidators. The company has been investigated for smuggling drug money to countries with secretive banking practices.
Gibbs looks in the container, but instead of it being filled with money, it has a bomb in it, timed to go off in under three minutes.
Just then, another hijacker shows up with a gun to the head of the Petty Officer. Gibbs tells him to release his hostage, and that he will only defuse the bomb after he does so, or after Gibbs shoots him.
The hostage is released, and the hijacker is arrested. The timer for the bomb counts down to zero but doesn't go off - Gibbs had already disabled it.
It turns out that the captain and Vilandro had schemed to steal the cartel's drug money - only, the captain double-crossed Vilandro and killed him. Then, he had moved the money to a different container and had rigged the bomb to explode, thereby destroying the hijackers and all evidence of his treachery.
Gibbs arrests him as he tries to recover his loot.