The third season opens in the aftermath of "Twilight", with the entire team in shock and Gibbs on a vendetta to seek revenge for Kate's murder.

Matters are complicated by the intervention of Gibbs' former lover and new NCIS director Jenny Shepard, and Mossad officer Ziva David.

The season finale introduces his former boss, Mike Franks (Muse Watson), who assists Gibbs in recovering from a near-fatal bomb blast.

A Navy lieutenant commander, who was in charge of a shipment of nuclear weapons, is thought to have been abducted leading to Gibbs and his team being called in on a Sunday to investigate.

The team discovers that the lieutenant commander had had a meeting earlier in the day at a shopping center and that she did volunteer work at an organization dedicated to combating online pedophilia, meaning that her abductor might not have been a terrorist but a pedophile she was tracking.