The film opens early on the morning of September 11, 2001 with the hijackers praying in their hotel room, then leaving for Newark Liberty International Airport. At the airport, the passengers and crew board United Airlines Flight 93 along with the hijackers. Shortly after boarding, Flight 93 runs into rush hour traffic, and the flight is momentarily delayed. The other 3 would-be-hijacked flights take off.
Eventually Flight 93 does take off and passes by Manhattan. Hijacker Ziad Jarrah catches a final glimpse of the World Trade Center before the plane gets airborne.
Air traffic controllers monitoring all current flights notice that American Airlines Flight 11 has taken a southern turn toward New York City. Not long after that, Flight 11 descends into Lower Manhattan and crashes head on into the North Tower of the World Trade Center, though air traffic controllers are not aware of it. CNN then broadcasts the first international shot of the smoking WTC. While the traffic controllers, unaware that Flight 11 has crashed, try to make sense of it, United Airlines Flight 175 begins to descend and turn toward NYC as well. Air traffic controllers then realize they are dealing with a hijacking. American Airlines Flight 77 is also hijacked. The traffic controllers alert the U.S. Air Force, who decide whether or not to shoot down all suspected hijacked flights. The traffic controllers and Air Force then watch in horror as Flight 175 crashes into the South Tower of the WTC on live television.
Word of the planes that hit the World Trade Center reaches Flight 93, and the hijackers then decide to begin the hijacking. One of them assembles a fake bomb out of clay and plastic, while the other 3 wrestle their way into the cockpit. In the cockpit they put a photo of the U.S. Capitol, their target, on the flight yoke mounted clipboard. By this time, Flight 77 crashes and creates a huge fireball at the Pentagon.
Much to the growing consternation of Ben Sliney and his people, coordination with the Air Force is haphazard and there are simply not enough planes ready, or armed, to respond to an in-air hijacking. Sliney ultimately decides to shut down all airspace in the United States and ground every single flight.
The hijackers do not prevent the people from making phone calls through the on-board GTE Airfone system. After hearing about the crashes into the WTC and the explosion at the Pentagon from loved ones, the passengers and crew understand that if they do nothing, they will also die, and eventually elect to storm the cockpit and attempt to retake the plane. The passengers make one last set of phone calls to friends and family, where they declare their intentions. The remaining crew assemble what makeshift weapons they can: cutlery, wine bottles, a fire extinguisher.
Learning that one of the passengers can fly a plane (although he has not flown a commercial aircraft), the group pin their hopes on him being able to at least control the plane. They debate whether the bomb is real or fake before deciding to start their counter-attack by overpowering the terrorist with the bomb. He is overpowered and killed by the passengers with a fire extinguisher. Having seen this, the terrorist in the forward section of the planes warns the two in the cockpit and makes several attempts to hold off the advancing passengers, including using what appears to be mace. He too is soon overwhelmed and killed by one of the passengers.
Ziad Jarrah shakes the plane violently to throw the passengers off balance, but nonetheless they make it into the cockpit. As the passengers wrestle for control, the plane goes into an angled nosedive towards the ground. The film ends just as Flight 93 crashes into an empty field.