The movie opens at an elementary school named William Dawes, in Lexington, Massachusetts, 1959. In the playground, we see Lucinda Embry (Lara Robinson) staring into the distance as if she is witnessing some catastrophic event. As she stares, whispering sounds are heard in the background. The teacher, Miss Taylor (Danielle Carter), repeatedly instructs Lucinda to come back into the class when the recess period ends. During the class session Miss Taylor tells the students that as part of the school's official Opening Day celebration, the students will draw what they think the future is going to look like, and place the results in a time capsule. She tells them this is Lucinda's idea (important later). As they start drawing, we see Lucinda in a trance, furiously scribbling seemingly random numbers onto a sheet. It appears that the mysterious whispering voices are controlling Lucinda's thoughts and actions. As she collects the students' work, Miss Taylor must grab the sheet from Lucinda due to her trance like state.
During the ceremony, we see a crowd gathered as the time capsule is lowered into the school grounds. In the distance we can see Lucinda alone and staring at the proceedings. A few minutes later Miss Taylor notices Lucinda gone from her spot, and her balloon floating off. This sparks a search party for her. Alerted by noise coming from a door to a school storage closet, Miss Taylor finds Lucinda inside, her fingers bloodied as she's scratched even more numbers into the wooden door. She is still crying and acting as if in a trance, before she begs Miss Taylor to make the whispering stop.
The movie then flashes forward to the present day 50 years later. We are introduced to M.I.T. professor John Koestler (Nicolas Cage) and his son Caleb at their house. John is cooking hot dogs for his son (who is holding a white pet rabbit). They talk about the possibility of intelligent life in outer space, and after dinner Caleb is in his bedroom watching his favourite show about tigers. As John tucks Caleb into bed, it's seen that Caleb thinks John's view on life life in outer space is tied to the tragic passing of Allison, John's wife and Caleb's mother. John kisses Caleb goodnight, and they go through a nightly ritual of using sign language for the phrase, 'You and me, together, forever;' Caleb is hearing impaired and uses a hearing aid (also important later). After Caleb is asleep, we see John drinking from a bottle of whiskey, and here we realize he is still coping with the devastating loss of his wife.
The next day we see John giving a lecture to his class about determinism. Determinism is believing that everything that happens in the world is caused by something that happened before it, a deliberate cause and effect. The flip side is everything that happens in this world, even evolution, was all random, accidental, and without any order. When asked by a student what he believes in, John replies, s**t just happens. After the lecture, he is talking to his colleague Phil (Ben Mendelsohn) when he realizes he is missing Caleb's school's 50th year celebration where they are opening the same time capsule shown at the beginning of the movie.
When he gets to the celebration he sees honoured guest Miss Taylor (now played by Alethea McGrath) giving a speech, and then the capsule is opened. Miss Taylor starts handing out the various pictures and drawings to the current students. As if by chance, Miss Taylor hands Lucinda's page of numbers to Caleb (all the other students get drawings of what the future would be like). As Caleb opens the letter and looks at it, he notices a strange looking man in the distance dressed in a trench coat, and starts to hear whispering voices in his head. This shows that there is some sort of tie between young Caleb and Lucinda as both can hear voices. Caleb takes the letter home.
During dinner that evening, John notices the unusual letter with numbers sticking out of Caleb's backpack. After realizing it was from the time capsule, he admonishes him for taking it, as it is still school property, and sends him to sleep. A few moments later, when John goes to Caleb's room for his customary tuck in, he notices Caleb watching old home videos of Allison singing him to sleep. Instead of tucking him in, John closes the door and starts drinking heavily. As he pours himself drink after drink, he accidentally overfills his cup and spills alcohol everywhere. He goes to the kitchen to find something to wipe up the mess with when he notices that he placed his cup over Lucinda's list. The upper left part of the circular mark left by the wet cup's bottom highlights a section of numerals: 911012996. John takes a close look these numbers, which catch his attention. He walks over to his chalkboard and writes these numerals on it. After a few tries of separating them in different grouping combinations with no meaning, he suddenly finds the first five numbers are the date of the September 11, 2001 terrorist attack. Looking the event up on the internet, he finds that the 2996 was the total number of victims. Startled, he writes the entire page of numbers onto the board, and with the help of the Internet, he finds the number groupings seem to predict the dates of every major catastrophic event of the past 50 years, in the chronological order in which they happen, along with the body counts, including the bombing of the Pan Am flight over Lockerbie, the Oklahoma City bombing, and Hurricane Katrina. There are a few groups of numbers left that are not circled and accounted for, meaning that these numbers may predict future events. Suddenly John's gaze falls on the number sequence 102708 and drops his drink in horror. It becomes clear that 10/27/08 is the date of Allison's death.
He tells his colleague Phil about the numbers and is met with ridicule, and John storms out of the office. Determined, John tracks down Miss Taylor and speaks to her at her home. He finds out about Lucinda, and how she disappeared, and how they found her in the closet when she scratched numbers onto the door (again, important later). Unfortunately, Miss Taylor tells him that Lucinda died a while ago. John hopes to get Miss Taylor to help corroborate his theory but it quickly becomes obvious that Miss Taylor, in her old age, has begun experiencing short-term memory loss that would make her word unreliable.
Later that afternoon we see Caleb playing soccer by himself in the front lawn. John is on the phone trying to hunt down more leads, when a black car filled with several of the mysterious looking strangers approaches Caleb. As the car approaches, Caleb starts to hear whispering sounds and thinks his hearing aid is malfunctioning. One of the men reaches out of the car window and hands Caleb a smooth black stone. John sees this and rushes outside but the men leave.
At his house, while looking up Lucinda's passing on the internet (her name is now shown as Lucinda Embry-Wayland, meaning she'd married), John is suddenly startled by his sister Grace (Nadia Townsend), who is worried about how he is still coping with his wife's death and how he doesn't talk to their father, who is a pastor. She offers to babysit Caleb so he can resume a social life. After a tense exchange of words, John asks her to leave.
That evening and throughout the night, John stays awake searching the latest television news updates for any possible catastrophic event that could be a part of the remaining groups of numbers, as the next day is one of the last three dates listed. One news update briefly lists disruption of cell phone satellite networks due to solar flares (important).
The next day John oversleeps and forgets to pick up his son from school. He calls Caleb and tells him he is on his way. On his way to pick up his son, John finds himself stuck on a highway in heavy rain, due to an accident. He phones Phil to apologize for their meeting earlier. He then uses his truck's GPS system to try and find an alternate route, but it shows that there are none. All of a sudden he notices the present latitude/longitude coordinates on the GPS system, and looks at Lucinda's letter and notices the same group of numbers immediately following the sequence that list the day's date. All the uncircled groups of numbers, as he now realizes, are the latitude and longitude coordinate locations of the disasters! He gets out of his truck and approaches the accident site. As he is talking to the police, an airplane comes careening out of the sky and crashes directly into the path of his truck before continuing on to the fields next to the highway, where it explodes. We next see a powerful and disturbing sequence of the aftermath of the crash. John does what he can to help the survivors, many of who are burning and in terrible pain, as explosions are still going off, before rescue workers hold him back.
When he gets home his sister is waiting for him with Caleb. He asks Grace not to tell Caleb what happened. In the background, a TV news report lists the death toll from the plane crash at 81 people, and we can hear a reference to navigational malfunctions due to electromagnetic radiation (important). Caleb repeatedly asks him what happened but John will not answer and Caleb storms off crying. Later that night Phil comes to see John. Shown that the uncircled dates are lat/long coordinates and knowing that John was at the site of the plane crash has severely rattled Phil. John is certain that the numbers are a warning for him, but Phil wonders if they're warnings to stay away, despite John being heavily occupied with two major disasters remaining in the number sequence.
Still later that night, Caleb is awakened in his room by one of the strangers, who points to the window. As Caleb goes to the window he is greeted by a horrifying sight, a terrible forest fire and hundreds of animals being burned alive. As he screams, John rushes up to his room to comfort him, and then he notices the stranger again outside the house standing by the trees. He attempts to confront him, but the man is gone by the time John gets outside.
The next day John and Caleb track down Diana Wayland (Rose Byrne) and her daughter Abby (also played by Lara Robinson). Diana is Lucinda's daughter. They are at a museum when John uses Caleb as a ploy to start a discussion with Diana. He invites her and Abby for drinks and they walk to the restaurant. There John reveals the truth that in fact it wasn't a random meeting, but that he tracked her down due to her mother and the page of numbers. He tells her the truth about the numbers, and wants her help. Angered by this deception, Diana storms off with Abby; paying only minimal attention as he tries to tell her that he was at the plane crash the previous day, and that tomorrow, 170 more people will die in New York City, and then 33 more on October 19th (important again). John pleads that he wants to save his son, thinking caleb is in danger, but Diana says she can't help.
Later on, John is at home when his attention is grabbed by a television news alert of a possible terrorist attack in New York (the camera pans outside his house to show several of the strange men standing outside). Checking the number groupings in Lucinda's letter, he finds that the coordinates show the corner of Lafayette and Worth streets in Manhattan. With a sense of urgency he anonymously calls from a pay phone and tells the FBI to block off the area.
The next day he has Grace babysit Caleb, and drives himself to New York on a personal mission to try to do what he can about the potential terrorist threat. When he gets to the corner of Lafayette and Worth, he notices it is not blocked off by the police. He angrily confronts a police officer, and then runs off to a nearby subway station to avoid being detained by the police, who begin pursuing him. Believing this is the area where an attack may occur, he starts scanning the area for any suspicious activity. As he walks down the platform he notices a suspicious looking man holding a large object underneath his jacket. As their eyes meet, the man suddenly sprints off, and John goes after him, believing him to be the threat, and a nearby police officer notices them. They both get on the train right before it takes off, followed by the police.
As they both near the front of the train, John starts warning people, particularly a young pregnant woman, to clear the train at the next stop. The police then catch up to them and try to arrest John. After John pleads his case that the man he was chasing is the threat, the police then switch their attention to the man. Frightened, the man drops what he was hiding: a bunch of DVDs he has stolen.
We next see the tracks being improperly switched due to electrical malfunction, and this causes the train to veer onto the wrong tracks and straight into the path of a parked train at full speed. The train goes off the tracks and creates a path of death and destruction as it careens out of control through the crowded platform. After the crash we see John solemnly walking out of the station along with other survivors, covered in dust. Even though he was not able to prevent the disaster from happening, this event to John is the final proof that the numbers are meant to predict past and future disasters. It also seems to indicate that for some reason he is the chosen one that discovered this. On the news reports later, an anchorman says that the track malfunction is believed to be related to the same electrostatic bursts that caused the Lexington plane crash (again, important). John gets home and tells Grace he got held up by work, but he will be by to pick Caleb up in 30 minutes.
When John gets back home, he finds Diana and Abby sitting outside his house. Diana is now sympathetic to him. She remembers what John told her about the date of October 19th (the date listed in the last grouping of numbers); Lucinda used to talk about that date often, saying it was the day that Diana would die. The four of them all drive to Lucinda's old trailer out in the middle of the woods to find more clues. As they drive, Diana reads the numerical list written by her mother, and how Lucinda's predicted date of Diana's death has haunted her all her life. She also talks about finding her dead body in the bedroom. John shares with her how Allison died. She died in a hotel room fire, and when she died he was out in the front of the house doing yard work. He tells her that he always believed that people deeply in love have a psychic connection even when apart, but when she died he felt nothing, and that is why he now believes in the randomness of things.
When they get to the trailer, they leave the sleeping kids in the truck and walk inside. As they near the front door, Diana is still reading the numerical list and pauses; she says Abby sometimes wrote things backwards and the final number on the list, 33, Diana believes is actually EE written backwards.
In the main room John sees numerous newspaper clippings of disasters around the world pasted on the wall. At the far end of the room he finds a drawing of Judgment Day with a picture of a large bright object in the middle. Diana talks about how she was nine when Lucinda died, and Lucinda always talked about hearing voices whispering terrible things to her. Lucinda moved out to the trailer to 'get ready,' although Diana never learned what for. Walking into Lucinda's bedroom, John notices a bible on the desk. As they are walking out of the room, he stumbles on something, and notices it's a smooth black rock similar to the one Caleb received earlier. He looks under the bed and notices more rocks, then looks at the underside of the bed. Noticing some writing, he turns the bed over to expose the underside of the bed. It is covered everywhere with the writing, Everyone Else (the EE from the last part of the letter). John then realizes that the final prediction will affect everyone on the planet.
At this point the mysterious strangers appear again and approach the truck, and we can hear the mysterious voices start to appear. Caleb and Abby watch the mysterious men converge on the truck. When Abby starts to open one of the doors, Caleb jams on the truck's horn, John and Diana run to the truck. Abby mentions that the men were whispering to her and we realize that Abby, too, has the gift to hear whispered voices. John grabs his gun and runs into the forest to confront one of the men. As he enters a clearing, he sees the man standing still facing away from him. He points his gun at him and orders him to turn around. The stranger does, and then opens his mouth as a bright shining light emanates from inside his body. This light blinds John and the stranger gets away. Back at home, Diana and John both say they believe strange men have been following them and their children for several days.
In the morning, Abby gives John the Judgment Day picture that was in the trailer. John notices that she had coloured in the shining object in the middle of the drawing and made it look like the sun. This is when it suddenly dawns on John that the final event is related to the sun. They all drive to John's lab office, where he meets Phil. John mentions to him about a hypothetical catastrophic solar flare model they worked on before. John says that in fact this model is of the earth, and that this flare will destroy all life on the planet. He tells Phil to go home and spend time with his wife.
As he walks out he tells Diana about the coming disaster, and she breaks down and says she wants to protect her daughter. They both agree that they will try to hide out this event by going to some remote caves not known to the public. Going back to John's place, they all scramble to gather clothes and supplies to take with them. John takes a moment to call his father on his cell phone. He tells him about the coming disaster, and asks him to take his mother and both find an underground shelter. His father refuses, saying that he is ready to die if it's his time. The cell phone then goes dead, obviously being affected by the solar flares.
As they are packing, John's thoughts go back to the last part of Lucinda's list, and he realizes that unlike the previous predictions, there were no coordinates. He then remembers Miss Taylor's discussion about Lucinda scratching numbers onto the closet door.
They all rush to the school, much to Diana's rising panic, as John breaks into the school and makes his way to the closet. He finds the closet but notices the door has been painted over. He takes the door off its hinges and brings it back to his garage. Using a heating gun and scraper John frantically tries to find the numbers, as Diana's panic rises to fever pitch. Thinking the solar flare could happen at any moment, Diana takes Abby and Caleb in her own car and drives off to the caves, leaving John. As soon as he finds the last set of numbers, he writes them down and runs out to his truck but realizes they are all gone.
Entering the numbers into the GPS he is shocked to find that the coordinates point to Lucinda's trailer. He takes off in his truck to find them. John is able to reach Diana on her cell phone, and he desperately tries to convince her to take both kids to Lucinda's trailer instead of the caves. He then drops the bombshell on her that this flare will penetrate miles underground and will kill everyone, making underground cave shelters meaningless, and that the only choice now is to go to the trailer. The conversation ends, and Diana stops at a gas station. As she goes to the pay window, she notices the television inside showing an emergency broadcast alert. The alert warns of the impending flare, and asks everyone to find underground shelter. As she is watching the alert, Caleb gets out of the car and calls his dad from a payphone. He is only able to tell his dad that they are at a gas station.
As Caleb is talking, he is taken by the mysterious stranger, who gets in Diana's car and drives off with the two kids. Seeing this, Diana runs after them in a near hysterical state, and jumps into an idle SUV at one of the pumps to give chase. During the chase she sees several cars ahead of her stopped at an intersection. She swerves into the opposite lane, and as she crosses the intersection she is violently t-boned by a huge truck, causing the SUV to flip over and we see her unconscious.
Next, John drives into the gas station and locates the pay phone Caleb used. He sees the same smooth black stone on top of the phone. He asks the store clerk if he saw a lady with two kids and the clerk tells him the kids were abducted and she gave chase. We can see that a large group of people at the gas station are already panicking and creating a small riot by looting anything inside they can carry.
John takes off in the direction of the chase, and he comes across the intersection where Diana was hit. He walks to the rear of the ambulance where paramedics desperately try to revive her with no success. As they call her time of death, John notices it is just past midnight, signifying that it is now October 19, the date of the final disaster and Diana's date of death predicted by her mother. After holding her hand and saying a few final parting words, John goes off to Lucinda's trailer.
When he reaches the trailer he notices tire tracks going off into the woods, and follows these tracks. When he gets to a clearing he notices the ground is covered in the exact same black smooth stones seen several times in the movie. Agonizing over his missing son, Caleb suddenly appears safe and calm, holding a white rabbit. He also finds Abby safe, also holding a rabbit, and she tells John that they (being the mysterious 'whisper people' strangers) told her that her mother is now in a safe place. We now realize that the reason why the stranger took Caleb and Abby was because Diana was not going to take them to Lucinda's trailer.
Caleb tells his dad that the mysterious strangers are taking them away, meaning to a safer place away from the impending catastrophe, and they were the ones who sent out the mysterious message so preparations could be made. We then see four of the mysterious strangers standing in front of them.
We then see a pattern of lights high in the sky, and then out of the clouds an enormous spacecraft emerges. The bottom opens up and a huge orb like transporter is beamed to the ground. It is now apparent that these mysterious strangers are beings from another planet, and that they have come to save this family. As they get ready to move towards the orb, John sadly realizes that the aliens came to specifically save Caleb and Abby, and not him. At first Caleb protests, but John convinces him that he will always be with him, and that he must go with Abby to be saved. After an emotional goodbye, Caleb and Abby walk towards the orb. As they do so, the strangers shed their human skins and reveal their true alien selves, bodies that give off bright lights. John and Caleb give a final heartfelt sign-language exchange of 'You and me, together, forever.' The orb goes back towards the mother ship and takes off into space. As the ship leaves the Earth, we notice hundreds of other ships also leaving, showing that many children from around the World were also being saved (John and Caleb's story was only one of countless others). John collapses on the ground, crying.
John is awoken the next day by a light rain and eerie orange glow in the sky from the solar flares. We see him driving through the city being destroyed by the approaching flare: buildings on fire, rising temperatures, and people running in panic throughout the streets, with whatever they can carry. As he drives on he sees Phil holding his wife on the street. He goes to his parents' home, where Grace hugs him. He tells her Caleb is in a safe place now. John goes to hug his father, Rev. Koestler (Alan Hopgood), who reminds him that this is not the end. Grace and Mrs. Koestler join John and Rev. Koestler in a group hug and hold onto each other as the final massive solar flare incinerates and vaporizes everything in the city. The last shot of Earth is from space as it is breaking up.
We then see what appears to be the landscape of a far away planet, full of odd colours, yet lush with plant life. The spaceship we saw earlier appears, and drops off young Caleb and Abby onto the surface with their pet rabbits before leaving. We see more spaceships arrive to drop more children, and the final shot is of Caleb and Abby running toward a huge and magnificent glowing tree in the background.