The story begins when Ness is awakened by a meteor that has plummeted to the earth near his home, whereupon he proceeds to investigate the crash site. When Ness arrives at the crash site, he finds a police roadblock and Pokey Minch, his friend and neighbor, who tells him to go home. Later, Ness is woken up again by Pokey knocking at his door, demanding help to find his brother Picky.

They find him asleep behind a tree near the meteor and wake him. Then the three encounter an insect from the meteor named Buzz Buzz, who informs Ness that he is from the future, where the "universal cosmic destroyer" Giygas dominates the planet. Buzz Buzz senses great potential in Ness and instructs him to embark on a journey to seek out and record the melodies of eight "sanctuaries," unite his own powers with the Earth's, and gain the strength required to confront Giygas.