At the New York airport, college student Chloe calls her mother Irene to tell her she’s home and learns that her father’s birthday party has been canceled because he was suddenly called to work. Since her dad is a pilot, Chloe decides to stay at the airport to find him. Meanwhile TV reporter Cameron is approached by a Christian lady who tries to make him accept Jesus in his life, claiming that all the tragedies he sees every day during his job can be explained by the Bible.
Chloe interrupts her to point out that God is punishing innocent people for the sins of the past and that “working in mysterious ways” isn’t an excuse. The lady walks away and Cameron thanks Chloe for helping him, so Chloe explains her mother is a religious nut too. In the parking lot, Cameron’s dad Rayford takes off his wedding ring before meeting with stewardess Hattie.
When they enter the airport, Rayford sees Chloe and rushes to hug her. However Chloe isn’t happy because she noticed he was flirting with the stewardess and calls him out since her parents have been having trouble in their relationship for a while. Rayford explains that they married very young and people change a lot through the years.
Since Irene got obsessed with religion, she's become impossible to live with. Noticing that her father is not wearing his ring, Chloe guesses that he took today’s job to be with Hattie. Rayford ignores the remark and gives her his car keys before leaving.
Afterward Chloe agrees to have coffee with Cameron and they discuss how crazy people are for thanking God for tragedies. Their conversation is interrupted when an employee brings her two tickets for U2 in London so she can give them to her dad, which took him two weeks to find. This proves he’s planned today’s trip in advance and it wasn’t a sudden call.
A frustrated Chloe gives the tickets to Cameron and asks him to do the delivery instead. While Cameron and Rayford get on the plane, Chloe goes to her dad’s car and finds his wedding ring. She goes home and after greeting her brother Raymie, she sits to chat with her mother.
At first the talk is friendly but when Chloe brings up the incident at the airport things get tense. Irene starts preaching and Chloe gets angry, so she walks off. Needing a distraction, Chloe ends up going to the mall with Raymie.
The boy is worried about their parents, but Chloe assures him things will be fine and they hug. Suddenly there’s a flash of light and Chloe finds herself hugging Raymie’s clothes because he’s gone. All around her, people find their loved ones missing.
As people panic all over the place, a car that lost its driver crashes right into the mall. Chloe takes a look inside and finds a dead person in the passenger seat. Soon people start to use the chance to loot shops and the bags of the missing people.
Outside a huge traffic jam has blocked the streets. On Rayford’s flight, some passengers try to make friendly conversation but others don’t want to be bothered. Once the plane is flying smoothly, Rayford sneaks out of the cockpit to secretly meet Hattie and show her the tickets Cameron gave him.
Suddenly the plane starts shaking and people discover that a bunch of passengers have disappeared. People start to panic as the plane loses altitude, so Rayford rushes back to the cockpit to discover his copilot is gone. He immediately takes over the controls to stabilize the plane.
Cameron begins recording everything as people lose their minds and begin pounding on the cockpit door, demanding to see the captain. Hattie fails to calm them down and Cameron tries to help her to no avail. Seeing this on the cameras, Rayford turns up the pressure in the cabin and the oxygen masks drop down.
The passengers have trouble breathing so they have no choice but to return to their seats and use the masks. Then Rayford tries using the radio to call for help but nobody answers, and his phone isn’t working. Once everyone’s calmed down, Rayford returns the pressure to normal and goes to talk to the passengers, using his authoritative voice to make them stay in their seats.
He reminds them that panic is their worst enemy right now, so they must stay composed until they get more information. Afterward Hattie realizes that her fellow stewardess is also gone and runs to the cockpit to ask Rayford for comfort since she’s having a breakdown. Since everyone is leaving their seats anyway, Cameron begins recording again and interviewing the passengers.
Nobody has seen anything strange and the vanishment happened instantly, only leaving behind people’s clothes. A panicking woman runs to the bathroom to consume some happy powder and comes back to her seat saying she knows none of this is real. Cameron tells her to go to sleep while noticing she’s written “it’s not real” on her hand.
A Muslim man thinks they should be praying but another passenger begins arguing with him because they have different Gods, so they can’t share their prayers. Before things can escalate, Rayford announces he’s flying back to New York. At the mall, Chloe manages to make her way through the crowd after lots of pushing and struggling.
She rushes to the parking lot to keep searching for Raymie but has to run off when a small plane suddenly crashes on the ground and destroys Rayford’s car. Chloe has no choice but to start walking, and when two bikers pass by they steal her brother’s bag. At that moment a crash happens on the bridge and a school bus falls off, landing on the river.
Chloe runs to help the passengers only to discover the bus is empty. Soon she reaches town and tries calling her house, but nobody answers. Cars are crashing all over the place and an ambulance comes to pick up the injured people.
Chloe runs to it thinking Raymie may be one of the victims and the police have to push her back. As Chloe continues to walk through town, the glass doors of a jewelry store suddenly blow up and a dead robber is thrown out. The store employee comes out with a gun and points it at Chloe until she runs away.
Soon she makes it to the hospital, where she notices a sign that says "the end is here". On TV, she watches the news and learns people have disappeared all over the country so chaos is spreading fast. The hospital is crowded with desperate people looking for their loved ones and Chloe can’t even get near the entrance.
She decides to go around the back and breaks a glass door to sneak in. Dodging the dozens of people in the corridors, she makes it to the nursery and discovers all the newborns are gone. As she checks the rooms, a mother appears behind her and tells her kids of all ages have disappeared, not only in the USA but in the rest of the world too.
Back to Rayford, he discovers a plane flying on the same flight path and tries to contact the pilot, but nobody answers. It turns out the other plane is missing both pilots but it still has a few passengers left. Hattie rushes to tell her passengers to put on their seatbelts while Rayford starts moving his plane, managing to tilt it just enough.
The crash is successfully avoided but the wing of Rayford’s plane still hits the other plane on its way out. Cameron looks out the window and notices the other plane going down in flames. One of the passengers uses the distraction to check the bag of the Muslim man thinking he may find the bomb that caused this, but it’s just an electric toothbrush.
Another man points out that humanity doesn’t have the technology to pull this off and thinks the missing people were abducted by aliens. Minutes later the passengers call Hattie to show her there’s something strange on the wing. Hattie makes Cameron take a picture and take it to Rayford, who concludes the wing is barely holding on and it’ll be hard to land the plane.
The autopilot isn’t working and Rayford can’t leave the cockpit, so he sends Cameron to check if anything is spilling from the wing. Cameron does so and confirms the plane is losing fuel. Another passenger notices this and starts to panic while a woman freaks out, saying she wants to go back to the place where her child disappeared.
Suddenly the wing catches on fire and the plane starts shaking, so people begin freaking out even more. Hattie and Cameron remind everyone it’s important to stay calm to avoid making the situation worse. Then Cameron updates Rayford, who explains he can’t do anything but try to make it to New York before they run out of fuel.
Eventually the fire goes out on its own and because of the amount of fuel they lost, they’ll have to start going down earlier than expected. When Chloe makes it back to her neighborhood, she finds lots of people grieving for their lost loved ones. Chloe hurries to her house and is devastated to find it empty.
Her mother’s jewelry is in the shower and the phone has a voicemail that is only static. When Chloe finds Irene’s Bible, she angrily throws it out the window. Then she goes to see the local pastor, who tells her this is the rapture and people who disappeared went to heaven.
He’s here because even if he spent all those years preaching, he never truly believed the words. God took all the kids and the believers to protect them from the dark times that will come soon. This only makes Chloe angrier and she screams at the pastor before leaving.
On the plane, Rayford checks his copilot’s things and finds a watch that says John 3:16, which is a Bible passage that claims people who believe in God will have eternal life. Hattie brings the other stewardess’ things too and they find a notebook with notes from Bible Study. Rayford concludes that this is the rapture and tells Hattie that his wife knew all along.
Hattie finds it ridiculous and storms off. In the cabin, a woman snaps and reveals she has a gun, asking the others to tell her the truth because she thinks they were sent by her husband to take her daughter. As Cameron tries to calm her down, the addict passenger shares that she went to a religious school and this incident matches the description of the rapture, so she thinks the missing people went to heaven.
The mother says she can’t live without her daughter and considers self-deleting, so Cameron shares some stories about his relationship with his mom until he changes the woman’s mind and takes the gun away. Moments later Rayford finally gets a response on the radio and learns the disappearing people happened around the whole world. The airport is full of crashed planes and it’s impossible to land, so Rayford will have to go inland.
Before Rayford can argue against these orders, the radio stops working again. Since Cameron has a satellite phone because he’s a reporter, Rayford asks him to call Chloe, but Cameron says he’s been trying all day to no avail. While showing him the sad note Chloe left on the tickets’ envelope, Rayford explains he wants to apologize to his daughter and admits it was never his wife’s fault that their relationship failed, it was his for walking away every time Irene talked about God.
Meanwhile a depressed Chloe climbs to the top of a bridge. After staring at the view for a few seconds, she apologizes to her mother for how she treated her earlier. When she’s about to jump, Cameron’s call finally reaches her phone and she gets to talk to Rayford.
They tell each other “I love you” and agree Irene was right. Rayford explains he isn’t sure if he’ll find space to land the plane but before he can say more, the phone loses signal and the call ends. Learning that her dad is alive is enough for Chloe to come down and run back to town, where she takes an abandoned bike to move faster.
At the same time Rayford tells the passengers about their low odds of surviving and asks them to start praying. While the plane starts going down, Chloe makes it to a construction site and gets on a truck to start clearing the area by pushing all the objects away. She tries calling Cameron and luckily the signal comes back, so she gets to tell her dad that she’s found a place for him to land.
The plane’s guidance system isn’t working so Cameron asks Chloe to open the compass app and give them the coordinates of her location before the call abruptly ends again. Cameron then puts the coordinates on his phone’s map, which Rayford uses as a guide to fly the plane in the right direction. However it’s still too dark for him to find the exact spot.
To make matters worse, the plane finally is running out of fuel. At that moment Chloe manages to connect their phones again and Rayford asks her for a big light since the truck isn’t enough. There are some gas tanks nearby, so Chloe covers them with fuel and throws a lighter, creating a huge explosion.
The flames are seen by Rayford and he starts descending in that direction. Chloe jumps back into the truck and tries to get out of the way, but she’s so distracted by the fire that she ends up crashing. The plane hits some cables as it goes down but it only causes some shaking.
Soon it reaches the ground and tilts because the back wheels haven’t come out. The tail and a wing are dragged through the ground, but Rayford manages to make the plane stand correctly and the wing goes up to avoid Chloe in the truck just in time. The plane slides ahead for a few more miles, hitting a bunch of things on the way.
It looks like it’s about to hit a huge gas tank too, but thankfully it stops before the worst can happen and everyone's safe. While the fire that Chloe started explodes again, Hattie takes out the inflatable slide so everyone can finally leave the plane. Chloe runs to hug Cameron and Rayford, who admits he should’ve never left.
She gives him both his and her mother’s wedding rings before everyone turns to look at the town in the distance, noticing all the fires. Cameron says it’s the end of the world but Chloe thinks it’s just the beginning.
