When a 6-year-old boy informs the NCIS team that his father was kidnapped, the team discovers that the missing father is actually a Lt. Commander working on a secret project named Honor, and that he is the only one who has the code that can open the project. While Gibbs gets closer with the boy, the rest of the team discovers that the project has been hacked in and the information inside has been deleted. Is the missing man innocent or is he actually the guilty one?

While working on an assignment, Gibbs is seriously injured in an explosion, and taken to a hospital, where he recalls his painful past, which he has always hidden from others. The rest of the team must proceed with the investigation and put their feelings towards Gibbs's injury aside. Tony is left in charge, which may cause a bit of trouble.

The NCIS team must work on an assignment against a terrorist group without Gibbs, who is still recovering from the explosion. Gibbs has to fight with memory loss, while he's visited by his mentor and his former boss. His help is needed, expecially when the team discovers that Gibbs is the only person who has informations about the terrorists' plans, so he needs to retrieve his memory before the terrorists attack.

Gibbs is forced to come back out of his retirement to help Fornell, who is being threatened by a convict that escaped from prison. The convict threatens both Fornell and his daughter Emily. Gibbs and the NCIS team re-open the convict's old robbery case, and question a retired sailor who is the only one who contacted the convict after he was sent to prison. The investigation will lead the NCIS team to a surprising discovery.

It's Halloween and the NCIS team is busy investigating a ransom case. A Marine's daughter has been kidnapped after the kidnapper attacked a Marine in his home. The investigation leads them to a fact that the couple has been separated. They decide to focus on the wife's ex-boyfriend, after learning that the woman is the one who destroyed their marriage. Meanwhile, McGee and Tony are stunned by Abby's Halloween costume.

Secrets arise when Gibbs former mother-in-law surfaces as a witness in a murder investigation.

Gibbs calls on the team to assist DEA Agent Luis Mitchell with a case that keeps going cold, but DiNozzo discovers there is more to Gibbs’ personal connection to the agent and his desire to help him succeed. Also, the team gossips about Gibbs’ new look after he replaces his standard military haircut and polo shirt for a modern cut and tailored dress shirt.