Twelve-year-old Ann Uekusa and her mother move to the small town of Shimane, where Ann's grandparents live and everyone seems to be familiar with everyone else. Ann soon becomes friends with Daigo, a young boy who lives in Shimane, as well as Fuji and Shika, Fuji's younger sister and her best friend in Shimane. When Ann's mother, Miwako, commits suicide, Daigo helps Ann cope with the sudden change in her life. They fall in love, but Ann's life can only become more complicated when her estranged father suddenly arrives from Tokyo. After greatly contemplating going to Tokyo to live with her father after he asks her, she decides to stay. Ann tells Daigo about her decision but makes her go anyway. Ann and Fuji both live in Tokyo but hardly ever talk because Fuji goes to an elite high school, K High. Ann met back up with her friends she had before moving to Shimane and they continue their friendships. In Tokyo, she ends up becoming closer to Fuji, which causes conflict between her and Daigo.In Shimane, Shika learns the truth about her parentage and in her confusion, she begins to fall in love with Daigo. When Ann returns to Shimane, Shika upsets Ann's fragile emotional state so that Ann and Daigo will break up. In the end, Ann breaks up with Daigo for fear that her own sadness will weigh him down. Ann returns to Tokyo and starts a relationship with Fuji; however, because she does not love him, the relationship does not last. Daigo refuses Shika and rumors begin to circulate that he is interested in his middle school classmate Ayumu, who has been helping him studying to get into university and become a teacher.Nearing graduation, Ann learns that her father and his friend Kaede Kuroki have been dating and she is pregnant with Ann's half-sister. Ann's father and Kaede marry after being encouraged by Ann and Ann's grandmother. Fuji, now aware that Shika was the child of his mother's affair rather than himself, supports her decision to studying abroad in Vancouver so that she can learn not to rely on others. Daigo and Ann make it to the post-secondary institutions of their choice while Fuji must repeat his senior year after running away from home.After attending her middle school reunion, Ann spends some time with Daigo, where he tells her to find her own happiness. Six years later, Ann meets a young businessman named Keiichiro Sakura and they become engaged shortly after. After Ann learns that he only uses people for his own gain, she confronts him about his insensitivity, but he is disappointed in her and breaks off the engagement. Almost a week afterward, she takes a train to Okayama, where Daigo teaches elementary school. Ann's grandmother, meanwhile, believes Ann will suffer the same fate as her mother. After a failed suicide attempt on the beach, Ann is taken to the hospital and later meets Daigo, who asks her to marry him. She says yes and at the very end the two are shown to be happily married with an infant son named Ryo. Meanwhile, Fuji decides to marry his cousin Mariko (against his family's wishes) and Shiika decides to work for her uncle in America.

Telly Paretta (Julianne Moore) believes that her son, Sam (Christopher Kovaleski), died fourteen months ago in a plane crash, but her husband Jim (Anthony Edwards) tells her that she's delusional and that they have never had a son and even her best friend Eliot (Jessica Hecht) doesn't appear to believe in Sam's existence despite her closeness to him. Dr. Munce (Gary Sinise) tells her that Sam was merely a figment of her imagination and is just imagining a life that might have been. He recommends that she be sent to a hospital, but she runs away and meets with a man named Ash (Dominic West) who she thinks is the father of a girl (Kathryn Faughnan) who was friends with her son and died in the same crash. At first he dismisses her, claiming he never had a daughter, and calls the police. After she is taken into custody, however, he remembers his daughter and rescues Telly. Together they escape and go into hiding, pursued by National Security agents. Telly and Ash capture an agent (Lee Tergesen), whom they threaten. The agent reluctantly reveals that he and other agents are merely helping "them" and that they do so to protect humankind. The roof of the house blows off and the agent, along with the roof, is sucked into the sky — presumably taken by "them"- and Telly and Ash flee. Eventually, Telly visits Dr. Munce again and he reveals that the disappearances are the work of "them," and that the government monitors their trials, all too aware that they have no power to stop "them" from doing whatever they want. Doctor Munce takes Telly to an airport and the dilapidated hangar of Quest Airlines, where he introduces her to an agent of “them” (Linus Roache). He tells the agent that “It’s over,” and to stop the experiment because it will only cause more harm. The agent replies, saying “It’s not over,” and then tells Telly that she has been a part of an experiment to test whether the bonds between mother and child can be diminished. In her case, her memories could not be erased. Telly refuses to deny her son's existence. The agent mentions that if he fails to erase her memory then he will look like a failure. The agent then subdues her and finally succeeds in erasing her memories of her son. During further questioning, though, a question about the name of her son triggers Telly's memory of her pregnancy, and all of her memories of Sam return. This causes the agent to be "abducted" himself, supposedly for his failure to erase her memory. This ends the experiment. Telly finds herself living a normal life, although she remembers everything that has happened. She reunites with Sam at a park. Also at the park is Ash, watching over his daughter. Like Sam, he has no memory of what has happened. Telly reintroduces herself, and the two sit and watch the kids play in the playground.