Aboard Air Force One, agent Caitlin “Kate” Todd has been on Presidential detail for a little more than a year and looks out for Navy Commander Ray Trapp, who has just been assigned to protect the President. Having met him before in the line of duty, the President invites Trapp to lunch in his cabin. Unfortunately, shortly after the meal, Trapp has convulsions and collapses. As a doctor tends to Trapp, Kate is immediately concerned about the possibly fatal implications for the President... particularly after Trapp dies.
Since Trapp is a Naval Commander, Gibbs and Tony are called to the plane, which has landed in Wichita. The President – who checks out healthwise – has been safely transferred to another jet, that will now be designated Air Force One, and is headed to his Los Angeles destination. Gibbs and Tony must then duke it out with FBI, local enforcement – and Kate – all who feel they have jurisdiction over Trapp’s body. Thanks to NCIS coroner Ducky, who has accompanied Gibbs and Tony aboard the plane, a ruse with the local coroner gives Gibbs and Tony the edge. Realizing that Kate can benefit the case since she can order the pilot to take off, Gibbs strikes a deal with her that they will jointly work together, and the plane departs... leaving FBI Agent Fornell furious to have lost this round.
As Gibbs and Todd survey the scene and Ducky conducts an autopsy, Kate reveals to Gibbs that Trapp had just received his “Yankee White” clearance. Now working for the President, he was actually back-up for Major Kerry, who would have been on the plane but had come down with the flu. With that discovery, Gibbs also learns from an embarrassed Kate that she was having an affair with her colleague Kerry.
The FBI leans on the Secret Service to have Trapp’s body turned over to them once the plane lands at Andrews AFB. Once the plane arrives, the FBI believes they have confiscated the body. However, NCIS has succeeded once again in dodging the FBI’s control by putting Tony in the body bag. With NCIS now in custody of Trapp’s corpse,
Gibbs swiftly puts forensic scientist Abby to work to determine Trapp’s cause of death. But her many tests only prove that Trapp was a health nut. On the surface, it actually appears that, somehow, the very healthy Trapp died of natural causes... which Abby refuses to believe.
With the President returning to Washington tomorrow evening, Gibbs is certain that terrorists have put some plan in motion with Trapp’s death. He asks Kate if he can tag along – and she agrees. Prior to take-off, the guilt-ridden Kate has a rendezvous with Kerry to break off their romance. In discussing Trapp’s death, she learns from Kerry that – once Trapp reported to the White House – he had given the new arrival some tips on where to find a good gym and dry-cleaners in the area. Soon after they tenderly bid farewell to each other and Kate leaves him at his car, Kerry convulses and collapses... in an eerily similar scenario to Trapp’s demise.
This Air Force One takes off, with a number of journalists, all who have been promised 10 minutes with the President because of the commotion surrounding Trapp’s death on the other plane. In the air, Gibbs learns from Tony via phone that Kerry is dead, and has to break the news to Kate. Through rounds of testing, the relentless Abby has discovered that Trapp – and obviously Kerry too – had received heavy doses of venom from a highly toxic Australian snake. Both of their uniforms had been laced with the poison in the collar and cuffs – probably from the dry cleaners they both used. Gibbs surmises that an Al Qaeda sleeper cell is responsible, which now has designs on taking down the President.
With this revelation, and knowing that Trapp’s death put them on a different aircraft than the regular Air Force One, Gibbs senses that danger is looming. Gibbs realizes that – with Trapp’s murder – they forced the President to fly his back-up, and that Al Qaeda has used that to their advantage. Gibbs thinks they have a vetted reporter aboard working in concert with them, who has somehow gotten access to the plane’s armory. Unfortunately Gibbs’ hunch quickly proves right: a journalist is convulsing and, while medics pass in that diversion, supposed reporter Leonard Rish – headed toward the President’s cabin -- pulls an MP-5. Armed and ready in the pandemonium, Gibbs battles and takes down Rish, thwarting the cell’s diabolical scheme.
After his success – which the FBI takes credit for – Gibbs learns that Kate, having broken protocol by having an affair with colleague Kerry, has resigned from the Secret Service. Intent on having her on his team, Gibbs offers her a job at NCIS.