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Follows a team of Naval Criminal Investigative Service (NCIS) agents who Investigate crimes related to the military and national security on the Hawaiian islands.

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.

Tennant and NCIS must take down a notorious team of international thieves using WWII explosives on armored trucks before they complete their final big job and disappear. Lucy and Whistler have a standoff about their previous encounter; and Ernie's mission in the field is more alarming than he expected.

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.

The wife of a naval weapons Officer disappears. The team investigates and find the man who took her, dead. She left the vicinity around the time the man was killed. They look into her background but Whistler tells them to back off. Tennant relents and with the info they have, she deduces the wife works for the CIA. They find her but her husband gets taken. Whistler wants to take her but to save her husband, they need her.

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.

A Japanese sailor is killed and evidence links the case to the murder of the victim's girlfriend back in Japan, NCIS must find the murderer before the wrong person is accused and the case triggers a diplomatic crisis.

The NCIS team investigates a cold case involving WWII-era bones on the 80th anniversary of the Pearl Harbor bombings, and are shocked to learn they belong to a 100-year-old survivor of the attack.

When a Navy petty officer is murdered, Jane and the team investigate while protecting the victim's friend and colleague.

When an anti-capitalist protestor is murdered, Jane and the team investigate and find themselves caught in a war between eco-activists and a tech billionaire fighting over a piece of land. Also, Jane and Captain Joe go on a date.

NCIS crosses paths with Whistler's team while investigating a shipping container filled with contraband weapons. Also, Tennant debates arresting Alex's friend's dad, knowing it will cause his friend to move away.

Evidence to put away a drug kingpin is stolen, Lucy goes undercover at an underground poker tournament to find out which high-roller is behind the crime. Lucy's feelings are in turmoil when Whistler's ex-girlfriend arrives in town.

NCIS team investigate the mysterious death of Navy engineer Joseph Chan, learning that the last person he met with was Maggie Shaw - Jane's mentor and friend, who has since been kidnapped. David Sola, a New Zealand intelligence officer who arrives in Hawai'i to follow a lead in a case that connects Joseph's death to a Chinese black op.

While Tennant investigates Maggie's kidnapping, she learns the shocking truth about her friend's past. She gets help from her team to prove what she found out is true.

Jane Tennant faces interrogation about her friendship with a CIA mole. Her team investigates an ultrasonic attack on a Marine team, the only victims at a crowded beach. Whistler has a new job that brings her into contact with Lucy again.

As Jesse enjoys a day sailing with his daughter, Gracie, pirates suddenly seize their yacht, take all the passengers hostage and attack Jesse, leaving it up to his team to quickly locate and rescue his daughter.

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.

When a ransomware attempt causes a dam to malfunction, Ernie and a team of hackers are tasked to find the culprit quickly, before all power and water is cut off on the island. Also, Lucy and Whistler work together, giving Whistler a chance to apologize to Lucy and mend their relationship.

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.

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.

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 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.

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.

Marine staff sergeant found dead in junkyard, investigation leads to illegal street racing underworld. Tennant suspects Alex is hiding something, Whistler anxious to introduce Lucy to co-workers.