Midway over the Atlantic Ocean, Marks gets text messages on his secure phone stating that someone on the plane will die every 20 minutes unless $150 million is transferred into a specific bank account. Breaking protocol, Marks consults with Jack Hammond (Anson Mount) the other air marshal on the flight. Hammond tells him it is a joke and to forget it. Bill reports to the pilot then watches the cabin cameras with flight attendant Nancy (Michelle Dockery) and Jen Summers. As he engages the text messager the woman scan for people also texting. There are 5 or 6 and Bill notes the names on the manifest. The last is Hammond who gets up and goes to the rear. Bill follows. They enter a lavatory and begin fighting, Hammond saying he needs the money. The fight is violent, Bil snaps the other air marshal's neck. This occurs exactly at the 20 minute mark, resulting in the first death. Bill closes the door and returns to the flight deck. He tells the pilot to contact the TSA with the info.
Now Marks has the lights on and announces to everyone a surprise inspection. He goes to each texter and checks their phones and pats them down. One is an NYPD cop, Reilly (Corey Stoll) Bill then notices the man,Tom Bowen ( Scoot McNairy), from the sidewalk at the airport, he roughly brings him to the rear galley, demanding to know why he lied about Amsterdam. Marks binds his hands with duct tape and puts him in a seat. Making his way forward the plane lurches downward. In the cockpit the pilot is having a seizure. Marks gets a Muslim doctor passenger to help but it is too late. When 20 minutes runs out again, Captain David McMillan (Linus Roache) dies of poisoning.
The public becomes convinced that Marks is hijacking the plane, as the bank account is in his name and a passenger has uploaded video footage of him treating passengers aggressively with no explanation. Co-pilot Kyle Rice has been instructed by TSA to ignore Marks and land in Iceland, the closest destination; he diverts the plane but continues to cautiously trust Marks. Bill finds that Hammond was carrying a briefcase full of white powder. Jen explains to Marks that passenger Zack White is a smartphone programmer. Marks has White design a hack which will cause the texter's cell phone to ring. Again forcing all passengers to sit with their hands up Bill rings the phone, he discovers it in the pocket of a passenger, who claims to have never seen the cell phone before. Taking him to the front galley Bill again roughs the man up, but the passenger dies in a similar fashion to the pilot.
Perplexed, and smoking in the lavatory, Marks finds a hole in the wall that allowed someone to an opening behind the pilot's seat; he finds that the most recently deceased passenger was struck with a mini dart. While Marks and Summers try to gain access to the texter's cell phone, it suddenly activates, sending automated messages to TSA implying that Marks is suicidal and is going to detonate a bomb on the plane. Marks finds the bomb hidden in the cocaine smuggled by Hammond. Meanwhile Reilly convinces some other passengers to subdue Marks. After a brief fight they have Marks pinned, but Bowen picks up the loose gun and has the others release him, then gives the gun back to Bill. Marks finally explains the situation to everyone and they agree to work with him. He attempts to initiate a protocol of least damage: by bringing the plane to 8,000 feet to equalize air pressure, placing the bomb in the rear of the plane, covering it with baggage and moving the passengers to the front in order to contain the explosion and minimize casualties. Bill starts to think this is not about the money at all, with only a few minutes before the bomb explodes.
Watching a video clip of himself roughing up the passengers, Marks notices Bowen slipping the texter's phone into the pocket of the second poison victim. Realizing that Bowen is the culprit, Marks engages him in a fight, and then Bowen explains he was appalled by the lack of security at U.S. airports before 9/11, hoping that framing Marks as a terrorist will lead to drastically increased security. His accomplice is Zack, who prepares a parachute. Bowen is prepared to die with the plane and shoots White, who expected to get off the plane with the money. The co-pilot dives the plane to 8000 feet, In the confusion Marks shoots Bowen in the head. White recovers and attacks Marks with a knife, but White dies in the explosion as Marks retreats to the front of the plane.
The co-pilot manages an emergency crash-landing at a military base in Iceland after the bomb explodes, disregarding orders from his fighter plane escort. the plane is damaged in the landing but there are no casualties, Marks and Summers save Becca. His TSA boss calls and apologizes and asks for the money back. Marks is hailed as a hero in the media, and the film ends with him and Summers beginning their friendship.