An experimental Naval aircraft crashes on Oahu, and Jane Tennant and her team must find who is behind it before classified state secrets are exposed.

Kai goes undercover with one of Hawai'i's oldest surf gangs when a petty officer who's trying to help wayward kids find a new path in the Marines is murdered.

When a marine is shot, the team investigates. They start by talking to him, he tells them that he went riding and he got shot probably by a hunter. They check out his story and learn he wasn't telling the truth. They go back to see him but he left the hospital, not fully healed. They learn a relative came and helped him. They see the relative, who doesn't know much but they find a bag filled with drugs. They think the bag belongs to his son. So they try to talk to him but he disappeared. They think the boy was asked by a drug ring to deliver the drugs but he changed his mind which means his father is trying to protect him. But the gang will stop at nothing to get them, so they try to find them. When Kai's father doesn't see his doctor, Kai needs to put aside his feelings to help his father.

Kai goes undercover as a chef in a local restaurant to gather intel on a notorious criminal kingpin who has a connection to the eatery.

NCIS Agents Nick Torres and Jessica Knight travel to Hawai'i when they learn a key witness in one of their old cases has turned up there with crucial evidence.

NCIS team investigates a shipwreck carrying exotic animals that now threaten the native wildlife on Oahu. Alex sustains a career-ending injury and Kai asks Melanie, a fish and wildlife agent, out on a date.

When a navy seaman is involved in a murder, the NCIS team is called to work the case on their day off. Also, Lucy finds out Whistler turned down a promotion in D.C. to stay in Hawai'i.

Captain Milius returns to Hawai'i for a secret prisoner exchange operation, and brings in Jane to be his personal security escort in the Philippines, where the exchange will take place.

Captain Milius continues to work with Tennant and her team in the aftermath of the prisoner exchange between U.S. and eastern Europe. Also, Whistler takes Ernie's advice and makes a grand gesture in the hope of winning back Lucy. First season finale.

Special Agent Tennant's team, along with NCIS agents Nick Torres and Jessica Knight, learn about plans for an attack in Oahu on RIMPAC (Rim of the Pacific); the world's largest international maritime warfare exercise.

The team's investigation leads to the world of illegal street racing after a Marine staff sergeant's body is discovered in a junkyard. Tennant's concerned Alex is hiding something from her, Whistler is anxious about introducing Lucy to her co-workers.

The NCIS team investigates the death of a Navy sailor and goes head-to-head with a ruthless local criminal organization. Also, Lucy looks for a new apartment.

A naval officer is murdered while moonlighting in community theater, the NCIS team recruits a familiar face to help lead them to a ruthless international killer. Kai enlists Whistler to investigate an old friend turned criminal.

In Washington D.C. to celebrate the retirement of a former professor. NCIS agents are forced to investigate the professor's suicide. Tennant, Jimmy Palmer and Sam Hanna are kidnapped, and it all ties into the mysterious suicide.

When Special Agent Pike is ambushed while working undercover with a local Japanese crime family, the team must find the person responsible for orchestrating the attacks.

When an elite special forces Marine captain is murdered, the NCIS team finds a suspect in a really unusual place.

Following a close call at a meth lab explosion, the NCIS team learn one of their own is being targeted. Lucy gets her first big case aboard her aircraft carrier.

When the murder of a captain and his wife echoes a previous case, the NCIS team brings in a former team member to help determine if they are dealing with a copycat killer.

A Navy deserter accidentally comes out of hiding, his family becomes a target that drives the NCIS team and Charlie 1 to investigate who is after them. Lucy surprises the team by returning to Hawai'i from her agent afloat job early.

Milius returns and asks Tennant to protect a girl who has info on a arms dealer the FBI and DOD want to arrest. Kai and Jesse are assigned and all she does is shop but it seems apparently That she has something else in mind. Kai tries to reason with her. Milius also reveals he was the one who got Alex into Annapolis. So he meets with her and Daniel which causes tension.

When Tennant interrogates a suspect during his helicopter transfer and the helicopter crashes, she must utilize her skills to save herself and the other passengers.