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.

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

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.

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.

Commander Chase is abducted from her home by an Army Ranger accused of murder, the NCIS team must act quickly to find her.

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.

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.