In 2009, the time capsule is opened and the drawings are given to the current students. A boy named Caleb receives Lucinda's envelope. His father, John Koestler, a widower and professor of astrophysics at MIT, takes interest in the paper and soon realizes some of the digits represent the dates and death tolls of every major disaster over the past fifty years, and suggests three disasters still to come. Meanwhile Caleb begins receiving visits from mysterious figures in overcoats, "The Strangers". During these encounters he hears their overlapping telepathic whispers.
John witnesses a commercial plane crash while on a freeway on the date that the paper had next predicted a disaster would occur, and he discovers that the unexplained digits on the paper are the geographic coordinates of the events. Speaking with Lucinda's former teacher, John learns of Lucinda's closet episode, and also that she had since died after a medication overdose. He then meets Lucinda's daughter, Diana Wayland, but is rebuffed once he mentions Lucinda's paper. But after John uses the numbers to correctly predict another disaster — a Manhattan subway train derailment which John tries and fails to prevent — Diana seeks out John, and together they go to investigate Lucinda's old remote mobile home. Having noticed that the last date on the paper is not accompanied by coordinates, further clues in Lucinda's home lead John and Diana to realize that the "33" listed as the death toll for the final disaster is actually "EE" reversed, which Lucinda meant to represent "Everyone Else." In the woods outside the home, John confronts one of the Strangers, who disappears in a flash of light and a deep, resonating noise. It is revealed that Diana's daughter Abby can hear the Strangers' eerie whispers as well.
John and a fellow professor forecast that a massive solar flare will soon reach Earth, and the final disaster on Lucinda's paper will most likely destroy all life on the planet. John then examines the door of the closet in which Lucinda was found and discovers it is where she had scratched another set of coordinates. They represent the location of Lucinda's old mobile home, and John decides it is somehow a refuge from the impending disaster. Diana insists they seek shelter in some little-known underground caves instead and she takes Abby and Caleb, without John's knowledge, to go there. As panic erupts after news of the flare is announced, the Strangers drive off in Diana's car with Caleb and Abby still inside. Diana steals a truck and gives chase but is killed when she is broadsided by a truck.
At Lucinda's mobile home, John finds the children with the four Strangers as a glowing vessel descends from the sky. The Strangers dispossess themselves of their human appearance and reveal themselves as glowing, translucent figures surrounded by wisps of light. The Strangers invite only those who can hear their whispers to leave Earth with them. John convinces Caleb to go with them, and the vessel departs with the two children. From the vantage point of space, similar ships are seen taking off from Earth, implying a future for the human race. John travels to Boston to be with his sister and parents. While he had distanced himself from religion, John reconciles with his estranged father, a Christian minister. John and his family embrace as the solar flare strikes Earth, vaporizing the ozone layer and incinerating all life on the planet. Elsewhere, Caleb and Abby are dropped off in an otherworldly field as other ships are visible along the horizon, dropping off others. The film ends as the two make their way towards a large, white, solitary tree in the distance.
