The story begins when a meteorite falls on a hillside in Onett, a small town in Eagleland. The main character, a boy named Ness goes to investigate the crash. There, he meets Buzz Buzz, an insectlike alien from the future, and learns that a cosmic destroyer named Giygas has set his sights on Earth and that according to an old prophecy, only Ness and three other chosen children can stop him.
The game then follows Ness as he travels from location to location, battling an unusual array of foes by traditional role-playing standards. Such foes include aliens, robots, walking mushrooms, personified objects like guitars and coffee cups, and hippies. Along the way, Ness meets friends like Paula, a girl with psychic powers, Jeff, a young scientist, and Poo, a mysterious Asian prince.
- Ness: A seemingly average boy from the town of Onett and the game's protagonist. Ness's primary weapon is a baseball bat but he can also use PSI for healing and attacking.
- Paula: A girl from Twoson, who has a variety of PSI powers used for battle.
- Jeff: A boy genius from Winters who can make useful machines from junk. He is the son of Dr. Andonuts.
- Poo: Prince of the eastern kingdom of Dalaam, who has trained in PSI and martial arts for the battle against Giygas.
- Porky Minch (Pokey in the English localization): Ness's self-centered next-door neighbor and recurring antagonist of the game.
- Dr. Andonuts- A scientific genius and Jeff's father. His invention, the Sky Runner proves useful to Ness and co.
- Mr. Saturn- A friendly race of strange creatures residing in Saturn Valley. Mr. Saturns have a small body with two eyes, a large nose, two tiny feet, catlike whiskers, and a single hair on which is tied a red ribbon. They help Ness and co. on multiple occasions.
- Apple Kid and Orange Kid- Two rival inventors living in Twoson.
- Buzz Buzz- An insectlike alien who comes to Earth to warn Ness about Giygas's invasion.
- Giygas- The principal antagonist of EarthBound, Giygas seeks to destroy Ness so he can spread his terror throughout the universe.
Political, religious and other topical elements
The game's main fictional national setting, "Eagleland", is a generally affectionate parody of the United States and its popularly-perceived stereotypical characteristics and customs.
The battle against the final boss, Giygas, which takes place in the past where he must be killed before becoming too powerful as he is in the present, is often theorized as a metaphor for abortion. Per this interpretation, the onscreen patterns of his distorted face supposedly form the outline of a fetus.
During the final battle, Giygas makes several off-color statements when damaged that sound similar to a person being raped. This had been deliberate as game creator Shigesato Itoi was basing it on dialogue from the Japanese film The Military Policeman and the Dismembered Beauty, which traumatized him when he stumbled into it when he was young.