"Mother" begins with the story of a young, married, American couple who mysteriously vanish from their small, rural town. Two years later, the husband, George, returned as mysteriously as he vanished, and began a strange study in complete seclusion. His wife, Maria, was never heard from again. Years later, in 1988 (changed to an ambiguous point in the 1980s in later releases), a young American boy named Ninten is attacked at home in a paranormal event. His father explains that Ninten's great-grandfather studied psychic powers, and asks Ninten to investigate a crisis occurring across the world, later revealed to be the work of an invading alien race. After finishing a few tasks, Ninten is warped to the world of Magicant, where the land's ruler, Queen Mary, asks Ninten to find her song, the Eight Melodies, and play them for her. Ninten returns to Earth and befriends a young boy, Lloyd, who is being teased at an elementary school. The two travel to the town of Snowman to deliver a lost hat to Ana, a young girl with psychic powers. Ana tells Ninten she saw him in a dream, and joins the party in hopes of finding her missing mother.