On the night of July 19, 1996, shortly after taking off from New York's JFK airport en route to Paris, TWA Flight 800 exploded over the Atlantic Ocean, killing all 230 people on board. After the crash, hundreds of witnesses came forward to say that they saw a light rising in the sky just before the explosion. This led many people to speculate that perhaps a missile hit the plane and caused the explosion. One theory was that it was friendly fire from military exercises that night. Other speculated that it was a terrorist act. Government officials later determined that the crash was caused by a mechanical malfunction and not by a missile. Author Nelson Demille bases his novel on the theory that a missile did in fact cause the explosion and that the government, for a reason that is not known, has engaged in a huge cover-up.

The novel begins on the night of July 19, 1996, on a secluded beach on a state park on Long Island. Lovers Bud Mitchell and Jill Winslow are married to other people and are having an affair. They drive out to the beach, where they find a sand dune, lay a blanket down on the beach and videotape themselves having sex. At some point, they go to the water to swim and point the camera towards themselves. At around 8:30, as Jill and Bud are at the water's edge, again having sex, Jill notices a light rising from some point in the ocean into the air. At the same time, a commercial airplane is moving through the night air. Jill gets Bud to look up, and they both watch as the light rising in the air heads directly towards the plane and then hits it, causing it to explode into a massive fireball over the ocean. Knowing that people will soon be coming to see what happened, and not wanting to get caught in their extramarital affair, Bud and Jill run back to the beach blanket, grab the videotape and take off in Bud's Ford Explorer. As they flee the scene, the videotape is still running, and Jill and Bud talk about what they have just seen.

The story next jumps to July 2001, exactly five years after the crash of TWA Flight 800, and the protagonist, ATTF agent John Corey, and his second wife, FBI lawyer Kate Mayfield, are arriving at the annual memorial service held on the beach for the victims and their families. The NTSB and federal agents have all officially determined that the crash was caused by a mechanical malfunction, but five years later, many people still believe that a missile took the plane down, either from friendly fire or terrorism, and that there has been a massive government cover-up. Kate worked on the investigation, and she is convinced that the crash was not caused by a mechanical malfunction. She persuades John to dig around about the case. At the memorial service, one of John's enemies, FBI agent Liam Griffith, walks up to John, tells him there was no missile and warns him not to get involved in the investigation. Another one of John's enemies is Ted Nash, but John and Kate both believe that Nash has been murdered by an Islamic terrorist.

John begins digging into the crash investigation. Kate leads him to several witnesses, who tell him about seeing a missile rising towards the plane before the plane exploded. A week into the investigation, however, the higher-ups at the FBI and John's NYPD bosses find out that he's snooping around about the TWA crash, when he clearly is not authorized to do so. As punishment for investigating the crash on their own without official authorization, John is sent to Yemen to conduct investigations into the USS Cole bombing, and Kate is sent to Tanzania to investigate the U.S. embassy bombing, which has been linked to the Al Qaeda terrorist organization run by Osama Bin Laden.

The story leaves off on the day that John and Kate leave for Yemen and Tanzania, and it picks up again on Friday, September 7, 2901, when John arrives back at the airport after his Yemen trip. That very night, John immediately continues his investigation into the crash. Through his NYPD cop friend Dom Fanelli, he is able to track down a woman who used to work as a maid at the Bayview Hotel, and through talking to her, he learns that the couple in the hotel rented out a videotape that they did not return. He figures out that the woman copied the videotape of the crash before the original taped was destroyed, and he goes looking for the woman and the tape. John eventually tracks down Jill Winslow, and she confesses that she in fact did make a copy of the videotape before Bud destroyed the original. John knows now that the FBI and other government agents have been lying to him and that they restored the videotape that Bud destroyed. They know that a missile hit the plane.

John whisks Jill to the Plaza Hotel in Manhattan, where Jill puts the videotape in the hotel safe. John and Jill hide out in the Plaza Hotel while waiting for Kate to return from Tanzania. John sets up a meeting with Liam Griffith and the other agents for the morning at the Windows on the World restaurant in the North Tower of the World Trade Center on September 11, 2001. On that morning, John, Kate and Jill all go in separate cars to the Trade Center. John is just walking into the plaza of the North Tower when the first plane hits the North Tower. John wanders through the rest of the day looking for Kate and finally stumbles back to his apartment, where he finds her alive. The next day, they go to the Plaza Hotel to retrieve the videotape, but they are told that there is nothing in the safe.