(Part 1) As Jane returns to work, having passed her medical and psych evaluations, she and the team investigate the death of a man, eventually uncovering a breach at the US Marshal's database that means the list of witnesses in WITSEC has been exposed and is on the dark web. Meanwhile, Sam Hanna from OSP in Los Angeles assists Jane with trying to cope with recent events and the murder of her friend, Charlie 1.
(Part 2) Following the crash of a prisoner transport plane, the NCIS team must find the convicts that escaped onto the island. During the apprehensions, Sam Hanna and Tennant are tasked by Swift to locate a high-profile Russian prisoner known as "The Chemist", a biological weapon maker.
When a robbery of a Navy Federal Credit occurs takes place in broad daylight, the team find themselves searching for a group of adrenaline-seeking thieves. Jane grows increasingly suspicious of Sam's reasons for having arrived in Hawaii.
The team investigate when a Navy pilot is found murdered at a local military resort with Lucy and Kate going undercover to find the mastermind running the criminal enterprise that's literally operating in plain sight. Meanwhile, Sam’s continued stay in Hawaii begins to annoy Jesse, who starts to feel sidelined.
The team is tasked to protect the daughter of a Russian oligarch carrying a deadly secret and is planning on defecting. Meanwhile, Sam asks Tennant for assistance in interrogating The Chemist for the latter’s remaining bioweapon locations.
When the fiancée of a vanished Naval officer seeks the help of NCIS, his secrets are exposed and go much deeper than she suspected. Meanwhile, Sam recruits Kai to be his exercise wingman.
When a Marine is murdered in the woods on the Big Island during training, the team tracks the suspect deep into the woods and discovers a disturbing secret. Jane gets a concussion during the search and encounters a mysterious figure in an isolated cabin.
When a Marine's wife is kidnapped for ransom, the team uncovers dark secrets while tracking down her abductors (who trigger Sam’s clown phobia wearing clown masks). Meanwhile, Sam asks Ernie's assistance decrypting a top secret computer program that could lead to major consequences.
When The Chemist is murdered in NCIS ELITE’s secret compound in Hawaii, Jane’s team and ELITE collaborate and find out a deadlier threat is in play.
In the series finale, following the ambush with that left the majority of the ELITE team dead, Jane and the team must track down a Filipino terrorist group and their targets.