A turn-based JRPG and sequel to then-Japan-only Earthbound Beginnings (1989) in which Ness, a young boy living in a land based on the USA, leaves home to go on an adventure through strange locations, get to know quirky characters and defeat an unknowable alien threat called Giygas while facing up to the realities of growing up and becoming familiar with the real world.

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 gets to the crash site he discovers 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 near the meteor sleeping behind a tree and wake him up. 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.