The peace of Hawaii is shattered when an experimental Navy aircraft crashes into a mountain, killing its pilot. NCIS Special Agent in Charge Jane Tennant and her team of NCIS agents Jesse Boone, Lucy Tara and Kai Holman along with NCIS computer specialist Ernie Malik, investigate the incident with the team wondering who's responsible for the crash.
When an armored truck is attacked with one of the guards being murdered and his colleague being left alive, Jane and the team find evidence that similar attacks have occurred all over the world. Meanwhile, Kai desperately tries to find a new home. Also, Lucy and DIA officer Kate Whistler engage in a standoff concerning their previous meeting.
When a Navy Petty Officer attempting to help wayward children find a new path by joining the military is shot dead, Kai goes undercover to befriend members of one of the oldest surf gangs residing in Hawaii to gain information.
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 th
When a Japanese sailor is found stabbed to death on a bench in downtown Oahu, the team discovers that the main suspect is also linked to the murder of the victim's girlfriend back in Japan. The team scrambles to find the true murderer before the wrong person is accused, which in turn could cause a diplomatic crisis between the United States and Japan.
The team investigate when a global star is kidnapped, only to discover that the supposed global star and her new husband aren't who they appear to be. The case putting the team at odds with Whistler, who has an agenda of her own. Meanwhile, Jane's old CIA mentor and friend Maggie Shaw comes to Hawaii to visit.
When a Navy Petty Officer is murdered, the team steps in to protect his girlfriend, a Coast Guard rescue swimmer, from any further attacks.
The body of an anti-capitalist is found in a field, with the team finding themselves being dragged into a fight between eco-activists and a tech billionaire seeking control of a piece of land. Meanwhile, Jane goes on a date with Captain Milius.
When the remains of a Navy officer who served during World War II are discovered in a cave on a beach, the team discovers that the remains belong to a hundred year old survivor who's going to be honored at a ceremony for the 80th anniversary of the Pearl Harbor attacks, even though the victim was thought to have been murdered eighty years ago. Note: This episode was dedicated to the Pearl Harbor victims and the survivors regardless of nationality or ethnicity.
The team investigate when a shipping container filled with contraband weapons goes missing, with the case leading them to cross paths with DIA officer Kate Whistler once again.
When evidence collected to help put a drug dealer away disappears, the team works with a Detective of the Honolulu Police Department to uncover who was responsible, sending Lucy undercover to an underground poker tournament. Meanwhile, Whistler's ex-girlfriend is in town, and Lucy finds herself struggling to come to terms with her feelings.
As the team investigates the death of a Navy engineer, the case turns personal for Jane when it's revealed that the last person he met before his death was none other than Maggie Shaw, Jane's mentor and friend who is later kidnapped. They find themselves working alongside an intelligence service case officer from New Zealand, who believes a potential lead in the case he's been working on could in turn lead them to a black op secret agent working for the Chinese.
As Jane continues working on the case of Maggie's abduction, she soon finds information that reveals her friend/mentor is not who she appears to be. Jane enlists the help of her team and Whistler to further investigate Maggie.
As Jane faces a committee who have questions for her regarding her friendship with Maggie Shaw, the disgraced CIA officer who was recently exposed as a spy working for the Chinese, the team investigate when a group of Marines fall ill with mysterious symptoms including damaged ear canals from a weapon capable of emitting ultrasonic waves.
Jesse's day of spending time with his daughter, Gracie is ruined when a group of pirates storm the yacht, taking everyone hostage. As Jesse fights to defend himself and Gracie as well as the hostages, his colleagues race to help save the hostages before it's too late.
When a hitman who murdered an NCIS agent and two FBI agents in Pittsburgh shows up in Hawaii, Kai goes undercover as a chef in a fine dining restaurant to track him down before more people are killed. Meanwhile, Jane and her ex husband Daniel find out their son Alex got into Amherst University, much to Daniel's disdain.
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.
Following the ambush that leaves the witness they were escorting dead with his body later disappearing during the resulting gunfight, NCIS Special Agents Nick Torres and Jessica Knight of the Washington, D.C. team works with Jane and the Hawaii team to find out who was responsible. ----
When a ship carrying exotic animals runs aground causing a shipwreck, the team work to find out the circumstances of the shipwreck and to find the exotic animals who might possess a threat to the wildlife on Oahu. Meanwhile, Jane receives news about her son Alex. Also, Kai asks 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 Hawaii to ask Jane and her team for help concerning a top-secret prisoner exchange that if exposed or interrupted in any way threatens to ignite a new Cold War between the United States and Russia.
Following the prisoner exchange, the team continues working with Captain Milius to determine who knew of the exchange and was responsible for the fatal poisoning of a Navy Commander.