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.

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.

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.

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.

The NCIS team investigates the death of a Navy sailor and goes head-to-head with a ruthless local criminal organization. Also, Lucy looks for a new apartment.

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.