After tricking his wife Marge into believing that the model for the Burly paper towel corporation Chad Sexington would have dinner with the Simpsons, Homer takes the family to the Pimento Grove to watch live performers as compensation. One of the acts is a hypnotist called Mesmerino. Homer volunteers, and Mesmerino hypnotizes him into thinking he is twelve years old again. As Homer starts to reminisce, he starts screaming incessantly all through the night. Mesmerino attempts to hypnotize him back into reality, but Homer still keeps on screaming. The next day, Homer's co-workers Lenny and Carl bring him home early from work, still screaming. They finally manage to calm him down with some Yaqui tea. He starts to recall the events leading up to the scream-inducing incident. In a flashback, Homer, Lenny, and Carl are hiking in the woods and are confronted by a young Fat Tony, but they are saved by a young Moe.
Upon noticing that his bar was empty, the present-day Moe arrives at the Simpsons' home. Moe remembers that while they sat by a fire, they saw a near-meltdown at the Springfield Nuclear Power Plant. The next day, they go to the old quarry for a swim, and Homer jumps in, only to find that there was no water but only mud. Though Homer admits that he remembers falling into the mud, he also recalls that there was no water in the quarry because something was blocking the inlet pipe. When Homer unblocks it, all the water came out and he finds a rotting corpse on top of his legs, causing him to scream incessantly.
Since Homer never told about his painful memory of the corpse to anyone, the Simpsons realise that it is still in the old quarry and decide to investigate. They go to the old quarry where they meet Chief Wiggum, who comes with them. Marge uses Burly paper towels to drain the water from the quarry. Then, they find the body, now a skeleton, and go into the inlet pipe to see where the body came from. They find that the pipe leads to a hatch which, in turn, leads to Mr. Burns's office in the nuclear power plant. They confront him about the body after he accidentally says 'corpse hatch' once they opened the hatch. Knowing that this would come, Burns confesses to them that the dead man is Smithers' father, Waylon Smithers, Sr..
However, Burns swore that he did not murder him, and to prove his point, he shows an old surveillance tape, filmed during the 1960s when Smithers' father goes into an unstable reactor core to prevent an imminent meltdown that would destroy the city. Smither's father succeeds in saving the city, but he dies of radiation poisoning, leaving Burns to raise Smithers as his own son out of empathy. Burns tells the Simpsons and Wiggum that he dumped Smithers Sr.'s body into the sewer pipe "since cover ups were all the rage back then", and that he kept the truth from Waylon Jr. because he was an infant back then; Smithers then enters the room, having heard the entire story. Burns apologizes to Smithers for lying to him, saying he wanted to spare him from the trauma of his father's real death. However, Smithers admits that he is glad that his father died as a real hero rather than being killed from a tribe of savage Amazon women, which Burns told him earlier. Declaring the case of the haunted quarry solved, Homer stores the skull in his "Memories" box, despite Marge's insistence to give it to Smithers, to which Homer responds that Smithers will just bury it again.