The movie starts with the hijackers in their hotel room. We see Ziad Jarrah sitting on the bed praying, and the other three are praying as well. Two pray on a rug on the floor. The youngest of the hijackers tells Ziad "It's time." They leave the hotel and catch a cab to Newark Airport.
We then see montages of people in lines to go through security and such. We see Captain Jason Dahl and his first officer board the plane and begin doing preliminary checks. The first officer heads outside to check on the fueling process and make sure everything is in order. We also see the flight attendants boarding the plane. The hijackers arrive in the terminal with their bags and they all clear security no problem. They head into the waiting area and sit down. This is intense as the camera pans to show all the various passengers that will be on the plane. With this comes the realization that the hijackers are sitting with the people they are going to kill. The announcement comes to start the boarding process, and everyone gets up.
The next scenes involve people arriving for work at the various tracking centers, including Boston Center. Small talk is had, weather systems are looked over, and the day begins.
Back on the plane, the passengers board and take their seats. Once everyone is on, the door is closed and the plane is pushed to the runway. Captain Dahl announces a thirty minute delay as there are other planes ahead of them. The hijackers seem agitated at this.
The movie begins going back and forth now between the plane waiting to take off and normal procedures at the various tracking centers. When we come back to the plane, they're finally ready to take off. As the plane takes off, we see a dramatic view of the twin towers out one of the windows.
Boston Center is monitoring all the flights in the air. We see American Flight 11 is one of them. Suddenly it stops responding to calls from Boston Center. After what seems like an eternity of this, Boston Center deduces there's a possible hijacking in progress. The weather tracking center is notified, as well as a military center. They continue to keep an eye on American 11. Back on United 93, the passengers are served breakfast and chat about their lives. The hijackers look a bit nervous and uneasy. Ziad Jarrah politely skips the offered food.
Back on the ground, Boston Center continues to monitor Flight 11. One of the controllers said he heard something in his ear that sounded foreign and was definitely not one of the pilots. He says they need to pull the tapes and send them to be analyzed. We then hear the infamous recording of Mohammed Atta's voice saying they have some planes. The tapes are given to someone to be analyzed.
On United 93, the hijackers are growing restless. The younger one moves into a seat next to Jarrah and tells him they need to do it now. He says it isn't the right time, and to go sit down. He will give him the signal when the time is right.
On the ground, the person who analyzed the tapes said he heard that they have some planes. Planes as in plural. At the weather tracking center, a worker says a flight attendant called in to say her plane had in fact been hijacked by men with knives. At Boston Center, American 11 then disappears from Boston Center's screen somewhere near Manhattan. They try to figure out where it went when suddenly another plane, Flight 175, stops responding to calls. The controller running the screen yells out that he thinks it's another hijacking. Back at Newark Airport, guys working in the control tower notice the World Trade Center is on fire. The weather tracking center gets CNN up on one of their screens, and they watch reports saying a plane hit the tower. At first everyone tries to figure out whether it was a small plane or a big one. When it's confirmed that it was a commercial plane, they all immediately realize it was probably Flight 11.
On United 93, one of the hijackers gets up with a backpack and takes it into the lavatory. We see him constructing a fake bomb made out of wire, clay, and a battery. He straps it on and then puts on his coat over it to conceal it. He then returns to his seat.
At Boston Center, Flight 175 turns off course and narrowly misses a Delta flight on the screen. They radio the Delta pilot and everything is ok with the Delta flight. After a bit of confusion, Flight 175 disappears. Back at Newark, the guys in the tower spot the plane heading in really low and fast. It slams into the second tower and everyone in the tower and at the tracking centers screams in horror. Chaos and confusion erupts, and suddenly reports of another hijacking come in. This time on one Flight 77.
On United 93 in the cockpit, Captain Dahl and his first officer get a bulletin warning of cockpit intrusion saying two planes hit the World Trade Center. Ziad Jarrah gives the signal. The youngest hijacker walks up behind a flight attendant and stabs her. The one with the bomb leaps up and stabs a passenger. Frightened passengers see the bomb and flee into the back of the plane. As a hijacker holds a flight attendant hostage, Jarrah tells her to open the cockpit door and nobody will be hurt. She uses the special knock to get in and the door opens. The first officer is stabbed, then Captain Dahl is stabbed. Jarrah takes over the controls, with another hijacker sitting beside him. They lock the cockpit door while the hijacker with the bomb keeps the passengers in the back of the plane. A passenger who is a medic is allowed to try to help one of the stabbed passengers.
At Boston Center, Flight 77 disappears from the screen. Reports come in of an explosion at the Pentagon. As the centers watch CNN reporting this, they realize they're at war with someone. Efforts are made to get fighter jets in the air, but they don't seem to be succeeding.
On United 93, the passengers are told they will be going back to the airport. However, one of the stewardesses sees the hijackers moving the bodies of the pilot and first officer out of the cockpit. She freaks out but continues to tell the passengers they're heading back to the airport. Passengers start calling loved ones to tell them they love them. They talk amongst themselves, one passenger saying he's been a pilot for years and something doesn't seem right here.
Back on the ground efforts are still being made to get jets in the air. The decision is also made to close the borders down and not accept anymore flights into the country. No exceptions.
The hijackers on United 93 see the bulletin about the World Trade Center and get excited when they realize the other targets were reached by their "brothers". One of the hijackers leaves the cockpit to tell the other two in the cabin the news. They get excited, and soon passengers learn about the World Trade Center via the phones they are using to call their loved ones. They also find out about the bodies of the pilots and realize they are not flying the plane anymore. Once they realize this is a suicide mission, they band together to do something about it. They're plan is to get the man that's a pilot to the front of the plane, give the controls to him, and then he'll hopefully be able to land the plane. One passenger tells the stewardess to go and get as many weapons as she can. She does and comes back with knives and forks.
Back on the ground, efforts are still failing to get jets in the air. One person sends some jets up anyway, even though it's against the FAA's wishes.
Back on United 93, the passengers wait until the hijacker with the bomb has his back turned. Suddenly, they spring up and attack him. A bigger passenger kicks him down, and they swarm him. They get the bomb and realize it's a fake. He is beaten to death and they storm the first class cabin. Ziad Jarah rocks the plane to try to throw them all of balance, but it fails. The younger hijacker uses a fire extinguisher on the passengers, but the bigger of them all gets through and tackles him. They grab the younger hijacker and break his neck. They then use a drink cart to bust through the cockpit door. The drag one of the hijackers out and kill him before storming Ziad Jarrah. The movie goes back and forth between the ground controllers and the passengers fighting with Jarrah for the controls.
The last thing we see is the ground outside the cockpit window get closer and closer.
The movie ends with words talking about how jets were able to get in the air, but it was too late. Nobody from United 93 survived. Then a tribute is given to all those who lost their lives on September 11th.