While his death is at first thought be to a tragic accident, NCIS eventually uncovers evidence suggesting the commander was murdered and that it might be connected to a possible assassination attempt on the President of the United States.
The NCIS team arrive to investigate the death, but meet some jurisdictional problems with both the FBI and Secret Service, who both want to take the lead.
During the trip, NCIS begin preliminary examinations when Agent Todd suddenly becomes ill. Gibbs is worried she too is infected with whatever killed the Commander, but she explains it is the same flu that Major Kerry had, revealing that she is in a relationship with him which is against fraternization rules.
Despite her protests, Agent Todd follows orders but Gibbs, having suspected such an eventuality, arranged for DiNozzo to take the place of the corpse in the body bag they turn over to the FBI, allowing their escape.
Back at the NCIS headquarters at Marine Corps Base Quantico in Virginia, Ducky autopsies the body of Commander Trapp, only to find he suffered a cerebral embolism, which is considered a natural cause of death.
While the team continues its investigation into the death of Commander Trapp, Gibbs and Agent Todd fly to the President's location to accompany him on the return trip to DC aboard the back-up Air Force One.
Soon afterwards, Major Kerry's corpse is discovered in his car in DC, with similar symptoms to those of Commander Trapp, and his body is taken to the NCIS lab.
After quickly determining that the current "football" carrier isn't in danger, Gibbs interrogates Agent Todd, as she was the last person in contact with both men before they died.
Gibbs find the armory open, grabs a gun and realises that one of the journalists aboard is trying to get to the President's quarters in an attempt to kill him.
At the end of the episode, Agent Baer thanks Gibbs for his hard work, and reveals that Todd has resigned from the Secret Service for breaking fraternization rules.
Together with Billy Webb (Director of Photography), Bellisario wanted to give NCIS a different look than other shows, starting with the first episode of the series.
FBI agent Tobias C. Fornell (portrayed by Joe Spano), who still is a part of the series, and medical assistant Gerald Jackson (Pancho Demmings).