A retired Navy diver named Diego De La Rosa dies in a decompression chamber, after first going berserk.
Ducky is disturbed to discover that he can't examine the body until the chamber is fully decompressurized - a process that will take four days.
Ducky decides to walk the diver's partners in doing the autopsy for him. He calls it a remote autopsy.
Tony uncovers secrets about each of the three surviving divers. One is deep in debt, another has been having a large number of phone calls to a burner phone, and the third was dishonorably discharged and her Army file is sealed.
Tony also tells Gibbs that the location of the ship is six miles away from an undersea pipeline. So the divers are definitely not working on the pipeline, as the ship's captain first said. The mystery is: what are they working on?
Gibbs confronts the divers. A lawyer named Jerry Grossman (who works for Olympus, the company that owns the ship) tells Gibbs that the divers have all signed a non-disclosure agreement. Grossman then tells the divers that if anyone says anything they'll be sued.
Sam Harper tells McGee he thinks Jalen Washington killed De La Rosa because he was having an affair with De La Rosa's wife Maria.
Gibbs confronts Maria about the affair. He shows her the burner phone found in her trash. She admits to the affair.
Abby tells Gibbs there was cocaine in De La Rosa's blood stream, mixed with red food dye.
Abby reveals that De La Rosa died of asphyxiation, due to mishandling of his re-breather air hose. He was taking in helium, but little to no oxygen. She tells Gibbs one of the other three divers definitely killed him.
Captain Hammond tells Gibbs he believes the murderer is Sam Harper. Harper was on a mission a few years ago when his partner almost died due to mishandling of a re-breather. At the time it was ruled an accident.
Tony reveals that one of the divers - Meredith Ragen - left the army after killing someone she thought was an insurgent. Turns out it was a translator. She agreed to leave the army under a dishonorable discharge, and they agreed not to press charges.
McGee reveals the secret mission of the ship (and the Olympus company): they are beta testing water-tight closets called PPAs that can be filled with weapons and supplies and sunk to the bottom of the ocean. They can be called up for immediate deployment when necessary.
Olympus was to deliver the final results of their testing to the Navy next week. They're worried that the murder case may scuttle the deal.
Admiral Morales tells Gibbs more about the PPA technology. He tells him the containers don't work, that they leak.
Abby shows the real mission of the ship: to use the PPAs to sink liquid cocaine to the bottom of the sea. As liquid cocaine is clear, they use red dye food coloring to indicate that the cocaine is still sealed.
The theory is that De La Rosa found out about the drugs, so someone slipped him some liquid cocaine, hoping he'd have a stroke or a heart attack. When that didn't work, someone mishandled his re-breather hose.
Gibbs arrests Meredith Ragen for the murder.
Gibbs interrogates Meredith, with Grossman acting as her lawyer. Gibbs points out that they found 200 vials of liquid cocaine at the ocean floor.
Gibbs also points out that she had a partner, and that there was evidence Grossman had been meeting with a drug cartel. He tells Grossman that they tracked a stash of liquid cocaine and followed it as it was raised from the ocean floor and put on a trailer, which was then raided by the DEA.
Tony comes into the interrogation room and arrests Grossman.