The hack takes place in an alternate timeline of EarthBound, where the Chosen Four didn't return in present day of 199X after the defeat of Giygas. The hack starts in Twoson where a bounty hunter Varik wakes up inside of Ness's house until he heard a strange man who told him to wake up and that he'll threaten him that he'll call the cops (implying that Varik was drunk). When waking up inside of a building of Sexy Sisters (formerly owned by the Runaway Five), a man reminds him that an ex-mayor of Onett, B.H Pirkle, needed him at the manager room for something important. There, B.H Pirkle told Varik that everybody is flocking over to the show place to just see him and then told a horrible news that a monster who went inside a house and violently killed a young girl's parents and urged Varik to investigate where the monster is and kill it for the sake of Twoson. The Bounty Hunter grant the key from the ex-mayor, promising him that once his mission is done, he'll be elected mayor. His mission begins by going into Sewers, in which it reveals the Sewer's top is already unlocked anyways even if Varik used the key.
As Varik traveled through the Sewers, a foul place filled with enemies such as rats and human scavengers. After battling with them along the way, he made it to a door that leads him into other side of the place with an unexpected terrifying twist that appears to be a no point of return: a horrendous Sewers where the dirty water turns into a pool of blood and walls turned from green to violet. He even sees even more gruesome and very disturbing enemies until he reach to end of the Sewer and onward to a black-and-orange landscape of Winters known as the "land of doom". From there, he made it to the laboratory of Dr.Andonuts as the narrator referring it a "metal coffin" and that the narrator said that it's making Varik's heart pounded, fearing what's going to happened next if he go opened the door. Varik touches the door of the laboratory and it's teleporting himself inside the quiet interior of the lab where it's just him and Dr.Andonuts. The doctor said the same dialogue as what he said from the original game with one exception: the death of his son. Starting to get a fearful thinking that Varik is being sent out from nowhere to kill him for what he had done, begging him to leave him be by teleporting himself into a realm of Magicant. Varik goes into a machine that appears to be as it appears to be an "ebb that's like the belly of a pregnant demon".
At this point, Varik has to make a choice whether or not kill Dr. Andonuts. The only apparent choice is "yes", since choosing the other, blank choice makes the narrator say it's not a choice and return to the selection screen. Choosing yes makes Varik kill Dr. Andonuts through the machine and which somehow kills Varik upon doing so, making the game to "end" early. If the player presses the B button, like the game's alternative title encourages, Varik gets into Dr Andonuts's mind, Magicant - his Magicant.
From there, Varik finds Dr. Andonuts's lost courage with few memory lanes of his past events (such as his abusive relationship with his unnamed wife and his operation on the Chosen Four as he claiming the Phase Distorter was a "death trap"), fighting 3 bosses and gaining the three out of four children from EarthBound - Jeff, Paula and Poo - as one states that their "death" were being transferred to the timeline where Giygas defeated, not the one where they're being sent from and aware that Dr.Andonuts been waiting for their return for the longest and the only thing what they can do now to "save" him. The four proceeds to the Sea of Eve .
After a very long journey through the Sea of Eve, Varik reaches to an area that looked just like Twoson just like in the beginning of the game and somehow Varik's mind is starting to take place temporarily as the people there are begs Varik that shouldn't have to kill monster and should leave this realm. Ignoring their requests and pleas, Varik finally enters Dr. Andonuts's brain right through between the trees. There, Varik and his party are now turned into the four main characters from Earthbound Beginnings (Ninten, Ana, Lloyd and Teddy) inside of the interior of the brain that strongely resembles the Devil’s Machine, but with blue-red palettes. As they reach to the brain's core, they meets Dr. Andonuts, whose appearance is now horrible, telling on how the world has done to him and made him a complete monster. The doctor proceeds on insulting Varik about him being a hero and that he's not really a hero because he "killed people for money" wondering where's the heroism in that. As his whole like been shaking with fear, he begs Variks not to kill him and leaves him alone but he wouldn't because he'll kill him anyway because that's what "heroes do; they have to kill the monster". From the words came out from from the Andonuts' mouth, Varik brought out a weapon as Andonuts starts panicking, saying that he'll make the monster cry, engaging a battle starting with Andonuts's Id, which doesn't use any attacks, but saying saddening words. After a depressing battle, Dr. Andonuts said the same dialogue like what Pokey/Porky said from his first defeat with Ness tthat he understands the four are already claiming to be heroes and "congratulates" Varik for killing the monster. He went on and said that he can feel the "blood from his brain leaking down to the rest of body" that it's making him sad. He then experiencing a strange effect upon Varik's killing of the monster and that his whole mind are filled with nothing but hatred and rage and then transforms into his new form with strange PSI powers, having blue aura around him.
Throughout the fight as Megalovania plays, Andonuts begins on cussing Varik out with excessive profanities as with he brought out various of deadly attacks and PSI. Varik and his party eventually defeat him as the exhausting Doctor admits of how weak he was and felt that he's better off dead. Before his passing, Andonuts to Varik that reminds him a lot of Ness and that the two will meet each other again, thus ending the battle. Afterwards, as the Bounty Hunter leaves the machine, he saw the corpse of Andonuts from inside the machine making the narrator mention that he didn't really have to kill him if there's a choice (which is not true - killing Dr. Andonuts is the only way to reach the end of the hack, though according to the making of the hack, the only way on avoid of killing Andonuts is by turning off the game). After leaving the lab, a SWAT team gave Varik an airlift back Twoson where everything turns back to normal just in time for Halloween.The hack ends with a ghost pooting on Varik's face upon sleeping to provide an anticlimax and Toby Fox thanking the player for playing the hack, stating that he had a blast making a hack and hoping that the player enjoyed it as the music Megalovania plays.
