When an ambulance explodes while carrying the remains of a Marine's body that was killed in a car crash, the NCIS team is called in to investigate what actually happened. The investigation leads them to some sudden discoveries -- the DNA of the victim found in the ambulance doesn't match the Marine's DNA; the ambulance was set up to explode; and the family of the dead Marine is hiding a very important secret.

The NCIS team must stop a teenage student from detonating a bomb attached to his body, while he's taking the other students hostage at a Quantico base high school. Gibbs tries to stop him when he enters the classroom, only to realize that there may be someone else controlling the teenage student from the outside. Meanwhile, while Gibbs is in the classroom, Tony is left in charge.

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.