NCIS gets called in to investigate a possible terror threat on trains after a guard is killed and perpetrators spoke Arabic. They find a piece of train equipment with the name of a recently fired employee on it. They track him, Rome, and his ammunition expert roommate, Bellamy. Rome was set up at work and fired because he spoke out about unsafe rail shipments.

Kensi and Deeks go undercover as Federal Railway Administration investigators to find out what's going on at the railroad company. 

Rome's mother gets a fake bomb sent to her to sidetrack the investigation. Meanwhile, Rome steals a train with four tanks of Chorine and heads into populated area. In the end, Rome never meant any harm, he was just going to showcase the dangerous shipment to out the rail line company.

Bellamy and a private investigator, Trager, set up a bomb on the rail line to cause the damage. Sam was able to disable the bomb in time. And, the train and shipment didn't cause any damage.

Bellamy and Trager were arrested.