Thirteen-year-old Jonah Skidmore, who was adopted as a baby, lives with his mother, father and his 11-year-old sister, Katherine. One day Jonah receives an anonymous letter in the mail telling him that he is one of "the missing." Jonah and his friend Chip believe someone who knows that Jonah is adopted is playing a prank on him. But the letter still concerns Jonah because his adoption records are sealed, and he knows nothing about his birth parents or the circumstances surrounding his adoption. He wonders if someone is really missing him.
That night, Chip comes over to Jonah's house in a panic. He, too, has received a letter, and after talking to his father, Chip finds out that he was adopted as well. Since Chip's parents refuse to tell him anything about his adoption, Jonah promises to help his friend.
Chip and Jonah break into Chip's family's safe; they find a note with the name and phone number for James Reardon with the FBI. Chip wants to speak to the FBI agent, but Jonah discourages him by pointing out that it was unlikely that the FBI had anything to do with his adoption. At dinner that evening, Jonah asks his parents if they could research his birth parents, and they agree to try.
Jonah receives a second anonymous letter. This letter tells Jonah to beware, because "they're" coming back to get him. Chip gets the same letter the next day. While the boys still hope the letters are a harmless prank, they realize that is unlikely because no one knows that Chip is adopted, and he has only recently moved to the neighborhood.
Jonah's father contacts the agency they used to adopt Jonah and finds out that Mr. Reardon is now listed in his file as having information about his adoption. Jonah's parents make an appointment with Mr. Reardon, who tells them that while they should not have been given his contact information, Jonah's adoption was routine. Mr. Reardon warns them not to ask too many questions and implies that Jonah was part of a baby smuggling ring. His birth parents may want him back. Jonah is overwhelmed and runs to the bathroom.
A janitor tells him to take a look at the file on Mr. Reardon's desk and memorize the names in it. Jonah does not remember seeing a file on the desk, but before he can ask more questions, the janitor disappears around the door of a stall. Jonah's parents and Mr. Reardon have stepped out of his office and into the hallway. Katherine sees a man appear, find a file from the filing cabinet, place it on the desk and then disappear. She thinks she has seen a ghost.
Jonah and Katherine work together. While he distracts Mr. Reardon, she takes pictures of the file with her camera phone. Later, Chip downloads the pictures to his computer.
There are two sets of names on the list: witnesses and survivors. Jonah's and Chip's names are listed under survivors. The children call all the names on the witness list. While almost everyone hangs up on them, a woman named Angela DuPre nervously asks them to never call her again.
They also call the survivors. Even though the group turns out to be made up of both girls and boys of different races, they are all 13 years old, were adopted, have received the anonymous letters and most live in the same area as Chip and Jonah. Some have recently moved to the area while others are in the process of moving there.
Ms. DuPre contacts Chip and asks to meet him at a room in the public library. Ms. DuPre tells Chip, Katherine and Jonah that 13 years ago, she was working as a gate agent for an airline when a plane materialized at her gate with a logo on the door that read Tachyon Travel. When she boarded the plane, she found 36 babies but no pilot or other adults. Several government agencies, including the FBI, came to handle the situation. After they removed the babies, the plane disappeared. Ms. DuPre believes Chip and Jonah were two of the babies and that the plane was really a time machine. She tells the children that she believes they were once older, maybe even adults, who traveled back in time, a process that changed them to babies.
As the children and Ms. DuPre are talking, a man tries to get into the room, and another man tackles him. Jonah and Katherine recognize the tackler as the janitor from the FBI building, the same man who put the file on Mr. Reardon's desk. The janitor (who the children call Janitor Boy, JB for short) tells Chip and Jonah to run. They escape through a window. Ms. DuPre decides to stay to get some answers. Feeling guilty about leaving her, Jonah runs back into the library to help Ms. DuPre only to look through the window and see her disappear in what he believes is a time warp.
When the children get home, they realize that all their files and lists of names and phone numbers are either missing or deleted from the computer. They suspect the time travelers have taken the information that can help them figure out what is going on. After a week of not being able to investigate further, Jonah's parents receive a flyer inviting them to a conference for adoptees, hosted by the county's department of social services. While Katherine thinks the meeting is a trap, Jonah is excited that they may be able to make contact with the other children from the survivors' list.
Chip attends the conference with Jonah's family, and when the attendees' names are being called, Jonah, Chip and Katherine quickly recognize names from the list. The attendees are split into groups, and Katherine notices that all the survivors are put in one group. She pretends to be one of them to get in.
The survivors are all led on a nature hike to a cave that has been modified with an automatic door to lock in its occupants. When Jonah tries to get out, he is tackled by a man named Gary, who is facilitating the hike. JB appears and starts to fight Gary. Mr. Hodge, the leader of the hike, shoots something that looks and sounds like a gun in the air to stop the fighting. JB chastises Mr. Hodge for bringing the device into the 21st century. As the men argue about violating the rules of time, Angela DuPre steps out of the shadows and shoots both Mr. Hodge and Gary with a Taser. Jonah picks up the object he thought was a gun, but JB tells him it is an Elucidator and asks Jonah to give it to him.
Not trusting any of the men, Jonah ties up JB as well and demands answers. Both Mr. Hodge and JB agree to give their sides of the story, and Mr. Hodge instructs Jonah to start a promotional film about his company, Interchronological Rescue. The film tells the survivors that ever since humankind achieved time travel, Interchronological Rescue has worked to right the injustices of history by rescuing children who were killed during history's catastrophic events, taking them to the future and offering them up for adoption. Because the children were as good as dead, taking them from their own time would not cause time ripples or paradoxes — significant changes in time that can alter the past or the future. The company also perfected age reversal techniques so the children would revert to babies and not remember their ordeals.
JB argues that while the company may have started with humanitarian intentions, it soon became a purveyor of prestigious names from history for rich people to brag about the pedigree of their adopted children. JB goes on to tell the survivors that Interchronological Rescue got sloppy and started taking children whose disappearances were noticed, causing several time ripples.
The survivors are the missing children from history, including Virginia Dare, Edward V of England, Anastasia and Alexis Romanov, and Charles Lindbergh III, among others. When Mr. Hodge took them from their original times, he caused a time crash that left them stranded in the present, and only 13 years later have both he and JB been able to come back for them.
Jonah also finds out that while Mr. Hodge and JB could not come back for the survivors for 13 years, they mailed the letters, left the notes with Mr. Reardon's name in the adoption files and told Jonah about the file in Mr. Reardon's office to create damaged time, small rifts that could be used to get closer to the survivors. Mr. Hodge wants to reverse the children's ages and deliver them to their adopted parents waiting in the future while JB wants to return them all to their original times in the past.
Most of the survivors, however, just want to return to their current lives, but JB tells them the present is off-limits; they must choose between the future and the past. While the survivors decide what they want to do, Mr. Hodge, Gary and JB are untied. Mr. Hodge gets the Elucidator and tries to use it to send the survivors to the future, but he is stopped by Jonah and JB. JB ultimately gets the device from Mr. Hodge and sends both he and Gary to time prison and tries to send Chip and another survivor, Alex, into the past. In an effort to stop JB, Jonah grabs the Elucidator, and both he and Katherine grab Chip. They all end up being sent back in time to the 15th century.
Speaking to Jonah through the Elucidator, JB tells him that Chip and Alex must remain in their time period in the 15th century, but Jonah and Katherine can cause even more damage by being in a time that is not their own. JB tries to instruct Jonah on how he and Katherine can return to the present, but Jonah refuses to do that without Chip and Alex. Jonah tells JB that he must give them a chance to fix the 15th century so they can all come back to the 21st century or they will mess up time worse than Mr. Hodge and Gary ever did. JB reluctantly agrees, wishing them good luck.