Telly Paretta (Julianne Moore) had a son killed in a plane crash with 10 other kids on the way to camp fourteen months previously. Telly is seeing a psychiatrist, Dr. Jack Muncie (Gary Sinise). Telly spends time at a dresser every day reminiscing. Her psychiatrist suggests she has to let go. The images of her son start disappearing. Her husband, Jim Paretta (Anthony Edwards), says this is good -- that she is coming back to reality after being delusional. The psychiatrist explains her son was delusional memories manufactured after a miscarriage. He recommends she be sent to a hospital. Telly insists her son was real. Telly goes to Ash Correl's (Dominic West) apartment to convince him that her son, Sam (Christopher Kovaleski), and his daughter, Lauren, played together. Telly finds a children's painting under his office wallpaper. Ash turns her in to the police. NSA Carl Dayton (Robert Wisdom) intervenes. Ash begins to remember his daughter, and decides to help Telly escape the agents. The NSA pursues both Telly and Ash, but they escape, reunite and discuss alien abduction. The NSA pursues and loses them again. Detective Ann Pope (Alfre Woodward ) wonders why the NSA is interested in missing kids. NSA agents meet Ann. The psychiatrist proposes a partnership with Ann to catch Telly.
Telly and Ash go to a country cabin and catch Al Petalis (Lee Tergesen) who indicates that the agents are merely helping "them" and it is for the protection of humankind. He mentions an experiment before the roof is ripped from the farmhouse and he disappears, presumably taken by them. Ann visits this country cabin after Telly and Ash have fled. The only evidence left behind is a note written on the window by Ash and Telly, explaining their children were abducted and pleading for help. Telly remembers that the airline her son was flying on that crashed was Quest Air. She and Ash check out Quest Air, which is closed down and being audited by an accountant appointed by the courts. They go on to the former CEO's house which is empty. Ann, still on their trail, follows them to the CEOs house. Ann sees a man at this house, and orders him to freeze. When he doesnt, she shoots him, but his bullet wounds heal within seconds. Ann then realizes Telly was telling the truth. She catches up to Telly before she flees again, and tells her she believes her and will help her find her son, when suddenly Ann gets sucked up into the sky. Ash and Telly leave together, and track down the strange man from the CEOs house. Ash attacks him, and the two struggle for a moment before Ash thrusts backward knocking both of them out the window together. Telly rushes to the window in time to see Ash get sucked up and the strange man disappear.
The psychiatrist finds Telly and takes her to the airport where the strange man is waiting. Telly then realizes the psychiatrist has been in cahoots with this man -- who seems to be an alien -- all along. The psychiatrist tells her that the government monitors the aliens trials- aware that they have no power to stop 'them' from doing whatever they want to do. The psychiatrist tells the alien man to finish the experiment and the alien says its not over and walks away. Telly pursues him and demands her son back. He tells her to imagine he is there. She then sees Sam behind the alien and tries to run to him, but he runs away and disappears around a corner. Telly chases him around the corner and runs into the alien who again insists that Telly forget her son. Telly realizes at this experiment was not about the children -- it was about the parents. The alien explains that the connection between parent and child is so strong as to be almost unbreakable. Almost. Every other parent in the experiment had forgotten their children except Telly. He says Telly must forget or experiment fails. The alien begins to choke her, and tells her to remember the first moment she ever saw her son when he was born. She does, and he steals the memory from her. She falls to the ground. The alien asks her the name of the boy she is looking for, and she replies, What boy? The alien looks triumphant and begins to walk away. Telly sits up and thinks about being pregnant, which causes her to remember again. She then, once again, demands the alien return her son Sam to her. The alien panics for a moment and says he needs more time for the experiment before being sucked into the sky. Telly runs home and finds Sam in a nearby park. Telly meets Ash, again, in the park, where each of them are watching their children. Everything is back to normal.