In 1959, student Lucinda Embry (Lara Robinson) hears whispers as she stares at the sun. When her class is chosen to contribute to the school's Time Capsule, each child is asked to draw what they believe the future will look like. Lucinda writes a page of seemingly random numbers and adds it to her elementary school's time capsule, which is set to be opened in 50 years. Lucinda's teacher calls for the pupils to finish but Lucinda continues before her teacher takes it off her desk unfinished. Lucinda then goes missing after the time capsule is dedicated, and is found by her teacher, Mrs. Taylor (Danielle Carter), in a utility closet scratching numbers into the door with her fingernails bleeding.
In 2009, Caleb Koestler (Chandler Canterbury) is a pupil at the same elementary school as Lucinda. When the time capsule is opened, Caleb is supposed to read and write about some of the capsule's contents. He's given the page of numbers written by Lucinda. His widowed father Jonathan (Nicolas Cage), a professor of astrophysics at MIT, notices the numbers have a specific set of sequences referring to the times, number of deaths, and locations of fatal disasters over the last 50 years, including 911012996 (the date and death toll of the 9/11 attacks). The last three sets of digits is the date that his wife died.
In the following days, a car drives by the family home with two strangers. They give Caleb a small smooth stone. Caleb later dreams of one of the strange men, who points to the window showing the world on fire with burning animals running out from a forest.
Jonathan tracks down Lucinda's daughter Diana (Rose Byrne) and granddaughter Abby. Though apprehensive and scared, Diana eventually decides to help Jonathan. She says that her mother used to hear voices and that the next date in the document, 19 October, was the day Lucinda always said Diana would die. Searching Lucinda's mobile home, they find pictures of the disasters she predicted, a copy of Matthäus Merian's engraving of Ezekiel's "chariot vision", and a pile of small smooth stones near Lucinda's bed. The last number in the document appears to be "33" but they notice that it is really "EE" written backwards. They figure out that EE also means "Everyone Else", representing a cataclysm that no one will escape.
Outside, more strangers walk up to the children waiting in the car. John drives them away only to have Abby say that the "whisper people" want her and Caleb to go with them.
The next day, Jonathan has a sudden revelation and rushes them to the MIT observatory, where he discovers that a massive solar flare will soon reach Earth, making it uninhabitable. Diana wants to hide in some caves. Jonathan reluctantly agrees at first, but Diana decides to take the children and heads for the caves without him.
While Diana stops for gas, an emergency broadcast is transmitted to alert the world of the solar flare. Jonathan calls Diana to tell her that the caves are not entirely reliable as the flare's radiation will penetrate a mile into the Earth's crust. While on the phone, the strangers take the children. Diana chases after them but is broadsided by a truck. Jonathan arrives to find the gas station in chaos as customers begin to panic and start looting the store following the broadcast. Jonathan arrives just as Diana dies at exactly midnight and finds the smooth, black stone in Diana's hand. He goes back to Lucinda's mobile home, finding the children and the strangers waiting in a dry river bed covered with the similar black stones. A space ship descends from the sky. Jonathan is refused entry but allows his son to leave with the strangers, who are revealed to be otherworldly beings, strongly hinted to be Angels. The ship departs with the children and a pair of rabbits, and a distant shot shows many similar vehicles leaving Earth.
The next morning the skies are on fire from the solar flare. Jonathan drives calmly while listening to classical music through the chaos within the streets of Boston, arriving at his estranged father's home. The TV is losing connection because the satellites are being destroyed in space. Together they embrace as the solar flare burns away the atmosphere. A wall of fire incinerates Boston and Manhattan and burns away the entire surface of the Earth, destroying all life on the planet. The Solar Flare keeps burning the earth until its nothing but molten rock. The Earth is then pulled into the Solar Flare.
Caleb and Abby are deposited by the beings on an Earth-like planet. In the final scene they are seen running through a beautiful field of grass towards a giant white tree which strongly resembles the Tree of Life.
- Nicolas Cage as Professor Jonathan "John" Koestler
- Rose Byrne as Diana Wayland / Lucinda Embry-Wayland (photograph)
- Chandler Canterbury as Caleb Koestler
- Joshua Long as Young Caleb
- Lara Robinson as Young Lucinda Embry / Abby Wayland / Young Diana Wayland (photograph)
- Nadia Townsend as Grace Koestler
- Ben Mendelsohn as Professor Phil Beckman
- Alan Hopgood as Reverend Koestler
- Benita Collings as Mrs. Koestler
- Adrienne Pickering as Allison Koestler
- Liam Hemsworth as Spencer
- Ra Chapman as Jessica
- Lesley Anne Mitchell as Stacy
- Gareth Yuen as Donald
- Verity Charlton as Kim
- Tamara Donnellan as Mrs. Embry
- Travis Waite as Mr. Embry
- D.G. Maloney, Joel Bow, Maximillian Paul, and Karen Hadfield as The Strangers
- David Lennie as Principal Clark in 1959
- Carolyn Shakespeare-Allen as Principal in 2009
- Alethea McGrath as Priscilla Taylor in 2009
- Danielle Carter as Priscilla Taylor in 1959