[[File:Mother 2 Crash Site.jpg|right|thumb|
200px|Buzz Buzz appears moments after a bright light engulfs the meteor]]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 road block 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 "[[Your Sanctuary|sanctuaries]]," unite his own powers with the Earth's and gain the strength required to confront Giygas.
After an encounter with some hostile gang members, Ness reaches the first sanctuary on a mountain above his hometown. He then proceeds to the next town, Twoson, where he rescues a girl named Paula from the Happy Happyist Cult and discovers that [[ Pokey Minch|Pokey]] (who has been the high priest of cult) is working against him. Together, Ness and Paula discover the second sanctuary . With the help of the [[ Runaway Five]], a band that Ness and Paula free from debt, the two arrive in [[ Threed]], where they are ambushed and captured. While in captivity, Paula sends a telepathic message to a boy named Jeff, who resides at a boarding school. Jeff responds to the message and acquires his father's [[ Sky Runner]], a flying vehicle, in order to reach Threed. After crashing the Sky Runner, Jeff rescues Ness and Paula and joins their group. The three of them travel to [[ Saturn Valley#In EarthBound|Saturn Valley]], a land populated by a strange race of creatures called [[Mr. Saturn]]s . There, the party learns that [[ Master Belch|a monster has been kidnapping the populace]] . Ness and the group proceed to defeat the monster and reach the third sanctuary above Saturn Valley. The party then travels through the desert to reach the next city.
[[File:Mother 2 Summers.png|left|thumb|200px|Screenshot depicting Ness, Paula , Jeff and Poo as they travel through Summers]] Upon reaching [[ Fourside]], the group again helps the Runaway Five out of debt and visits a department store only to have Paula kidnapped. Ness and Jeff proceed to find her, and along the way, destroy a hallucination-projecting relic called the [[ Mani-Mani Statue]]. The two boys continue their search only to discover that Pokey and the Mayor have taken Paula. However, because Ness and Jeff defeated the Evil Mani-Mani, the mayor returns to normal. Pokey escapes in the Mayor's helicopter and Paula rejoins the group. After returning to Threed, Jeff repairs the Sky Runner, and they set flight for Winters to discover the fourth sanctuary. The group then cross the ocean and arrive in Summers where Ness falls unconscious and dreams of a far-off land known as Dalaam. There, a young prince named Poo has completed his training and is instructed to join the party on their journey. The group then returns to Fourside and are able to discover the fifth sanctuary.
The four then procure a boat and travel to [[ Scaraba]] where they explore a pyramid in the desert. Ness and the group then travel to [[ Dalaam]] and find the sixth sanctuary there, after which they acquire a submarine and travel into the [[ Deep Darkness]], a path leading them under the earth. There, they find [[ Tenda Village]], a small community populated by extremely [[ Tenda|shy creatures]]. After acquiring the [[ List of key items in EarthBound#Shyness book|book of overcoming shyness]], Ness is able to speak to the shy villagers who allow them passage to the [[Lost Underworld]]. There, they discover the last two sanctuaries.
activating the final sanctuary , Ness falls unconscious and enters a strangeworld composed of his dreams, [[Magicant#In EarthBound|Magicant]]. There, heencounters [[Ness's Nightmare|his nightmare]]. After defeating it, Magicantvanishes, and Ness becomes much stronger because he has conquered Giygas's influence over him. After awakening, Ness and the group return to Saturn Valleywhere Jeff's father, [[Dr. Andonuts ]], has finished the Phase Distorter, a timetraveling device. Dr. Andonuts explains the kids that the machine cannot warp themto the past in their current form since life cannot withstand the warp through time. In other words, time travel would likely destroy their human bodies. Toremedy this problem, Dr. Andonuts proposes to them to have their soulstransplanted into robotic bodies, warning them that he doesn't know whether or notthe process is reversible. Despite this critical warning, Ness, Paula, Jeff andPoo are willing to take the risk. Now in the form of robots, Ness and his friendsuse the [[Phase Distorter ]] to travel to the past where they encounter Pokey and Giygas, who , in order to contain his massive power, has been sealed inside the Devil's Machine. Pokey informs the group that Giygas became so powerful that hismind was completely destroyed, referring to him as an "all-mighty idiot". The groupdefeat Pokey, who then shuts off the Devil's Machine and releases Giygas, trappingthe kids in a chaotic dimension composed of his own indefinable being. Since Giygasis too powerful for Ness and his friends to overcome by fighting, Paula begins topray, reaching out to the inhabitants of the Earth, including family members andfriends, who all pray for their safety, and eventually, she reaches out to theplayer. The combined prayers of both Earth's inhabitants and the player reachGiygas and exploit his weakness, which turns out to be human emotions. As a result,Giygas vanishes from existence . with all the damage he had done to Eagleland andthe rest of the Earth erased from history, the souls of Ness and his friends departfrom their robot bodies, travel back to the present and return to their respectivebodies. After bidding each other farewell, the heroes return to their homes.
After the ending credits, Picky Minch comes to Ness's house in the middle of the night and gives him a letter from Pokey that says "''Come and get me loser. Spankety, spankety, spankety!''", and the game ends with him and Ness pondering what has become of him.