While investigating the deaths of a diver and a captain, Gibbs and company meet two special agents of the Coast Guard Investigative Service, who present similarities to the gang. They all cooperate, find the truth, and nab the bad guys.

A Marine first lieutenant dies of gunfire during a dinner cruise; Abigail Borin, of the CGIS, also is a guest during the same event; she, Gibbs, and the gang investigate together. They find and fit the pieces, and they nab the bad people.

A boarding party from a Coast Guard cutter visits a foreign-flag cargo ship; no crewmember is visible, but a gunman kills a petty officer. The NCIS and the CGCIS investigate. Gibbs, Borin, and the gang sort it out and serve justice.

An inflatable raft washes ashore with three survivors from a missing Navy helo; the pilot also is missing; Gibbs and company plus Borin (of the CGCIS) investigate. The team and the other Abby find the pilot, the truth, and the chopper.

An explosion and a fire damage an offshore drilling platform near the Virginia Capes, killing one (a major in the US Marine Corps Reserve) and injuring many others; Gibbs and company, along with Abby of the CGIS, investigate. The CEO and the chief legal counsel of the oil company assure the SecNav and Gibbs of their utmost cooperation. Tony and McGeek trace one lead, which appears to reach a dead end, but which leaves egg on McGoo's face; Gibbs and the other Abby suspect that the target was not the platform but rather the dead victim. Tony and McGee plus Gibbs and Borin revisit the dead end, where they make a major discovery; Abby puts things together in her shop; Borin questions the corporate lawyer in Gibbs's chat room and brings the investigation to a close. Meanwhile Halloween pranks abound, eventually tripping even Tony.

While the NCIS team is on a training exercise with CGIS Special Agent Abigail Borin, Gibbs spots a man overboard. It leads him to board another ship called The San Dominick, and he soon discovers that it has been taken over by pirates.