University of Southern California student Chloe Steele has traveled back home to surprise her father, pilot Rayford Steele, on his birthday. However, her excitement is short-lived when her mother, Irene, calls to inform her that Rayford won't be able to attend the celebration. While waiting at the airport, Chloe crosses paths with investigative reporter Cameron "Buck" Williams.
When Rayford arrives shortly before his flight, he apologizes profusely to Chloe, claiming he was summoned to pilot a last-minute flight to London. He insists that everything is alright with his wife, who has recently embraced Christianity, much to Chloe's dismay. Yet, Chloe's intuition tells her otherwise; she has witnessed Rayford's flirtation with flight attendant Hattie Durham and notices his wedding ring has mysteriously vanished. Her suspicions are soon confirmed when she learns from an airport employee that Rayford ordered two coveted U2 concert tickets in London, suggesting his trip was premeditated and possibly romantic.
Disregarding her mother's Christian teachings, Chloe takes her younger brother to the mall, where the unexpected occurs—her brother suddenly disappears, leaving nothing but his clothes behind. This shocking event triggers chaos as other shoppers begin looting, and destruction ensues— a driver-less car crashes through the mall windows, while a small, unpiloted plane lands in the parking lot. As Chloe watches the news, the gravity of the situation dawns on her; children and adults alike are vanishing, and panic is spreading globally.
Meanwhile, aboard Rayford's flight, a similar phenomenon unfolds. Passengers—including his co-pilot Chris Smith, the flight attendant Kimmy, and all the children—have inexplicably disappeared, leaving nothing but their belongings. As panic sweeps through the cabin, Rayford attempts to calm everyone, assuring them he will keep them updated with any information. Struggling to establish communication with the ground, he eventually learns of the widespread disappearances and the ensuing chaos. Just then, a pilot-less jet approaches him, causing a harrowing near-miss that damages his fuel line, prompting him to consider a desperate return to New York.
On solid ground, Chloe hears her father's distress signal and fears his plane has crashed. Her worries escalate when she uncovers her mother's jewelry abandoned in the shower, further confirming her family's peril. Seeking answers, Chloe heads to New Hope Village Church, where family pastor Bruce Barnes reveals a shocking truth: God has taken His believers to heaven, leaving the rest to endure the apocalypse. Bruce admits he remained because his faith was not genuine. At the same moment, Rayford realizes his co-pilot and stewardess's personal belongings echo the pastor’s revelations. He confides in Hattie about his wife, initially upsetting her upon learning of his marriage. However, he urges her to muster courage and aid in calming the frightened passengers.
In a moment of despair, Chloe climbs a bridge, contemplating ending her life. Just then, she receives a call from Buck, who has joined Rayford in the cockpit. Rayford informs Chloe that all New York airports are closed, traffic is gridlocked, and their fuel reserves are critically low. Driven by determination, Chloe finds an abandoned Ford truck and clears a makeshift runway from construction equipment on the bridge. Utilizing her compass app, she coordinates their landing site. With her guidance, Rayford successfully glides the plane to a rough landing, saving all aboard. As the passengers disembark, they are met with a devastating sight of destruction. Buck observes that it appears to be the end of the world, but Chloe asserts that it is merely the beginning.
