An experimental Naval aircraft crashes on Oahu, and 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. Also, Kai searches for a new place to live; Lucy and Whistler have a standoff about their previous encounter; and Ernie's mission in the field is more alarming than he expected.

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.

When a Japanese sailor is killed on American soil and evidence links the case to the previous 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.

When Tennant and NCIS are tasked with finding a kidnapped globe-trotting social media star, they find that she is not who her husband, or her followers, think she is. Also, the team is at odds with Whistler, who has an agenda of her own.

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.

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.

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

When 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. Also, Lucy’s feelings are in turmoil when Whistler’s ex-girlfriend arrives in town.

When NCIS investigates the mysterious death of a Navy engineer, Joseph Chan, they learn the last person he met with was his colleague, Maggie Shaw, Jane’s mentor and friend, who’s been kidnapped. Also, David Sola, a New Zealand intelligence service case officer arrives in Hawai’i, following a lead that connects Joseph’s death to a Chinese black op secret agent.

While Jane investigates Maggie’s kidnapping, she’s shocked when she learns the truth and enlists her team and Whistler to prove her findings.

While Jane is questioned following Maggie Shaw’s arrest, the rest of the team investigates a mysterious case of Marines with damaged ear canals from a weapon that emits ultrasonic waves. Also, Ernie visits his friend, Dr. Tony Lee (Alec Mapa), to identify possible suspects who had access to his classified weapon.

As Jesse enjoys a day sailing with his daughter, 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. Also, Jane discovers that a school on the mainland has recruited Alex on a baseball scholarship, which he's kept secret from his family.

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.

The crossover starts on NCIS S19E17 Starting Over (I).

The NCIS team investigates a shipwreck carrying exotic animals that now threaten the native wildlife on Oahu. Also, 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.