With Burns in the hospital, the Springfield police search for his assailant. Smithers vaguely remembers shooting someone the night before in a drunken rage. Guilt-ridden, Smithers heads for a local church, and is promptly arrested when the confessional turns out to be a police sting. While passing the media on his way to the police station, Smithers makes a witty remark Sideshow Mel recognizes from an episode of Pardon My Zinger that aired at the same time as the shooting. Mel realizes Smithers must have watched it as well, giving him an alibi. As Smithers's memory clears, it turns out he had actually shot Jasper in his wooden leg. Meanwhile, the townspeople pull down the sun-blocker, which crushes Shelbyville to their delight.

With one of the prime suspects cleared, the police, aided by Lisa, eliminate other suspects, including Puente (whose revenge took the form of a "slanderous mambo"), Skinner (who was found by Chalmers to be applying what he thought was camouflage make-up at the time of the shooting), Willie (who cannot fire a gun due to arthritis in his index fingers), and Moe (who is cleared via polygraph test). After a surreal dream about Lisa, Chief Wiggum finds an eyelash on Mr. Burns's suit which matches Simpson DNA. At the same time, Burns wakes up from his coma, exclaiming "Homer Simpson!" The police raid the Simpson home and find a gun under the seat of their car, covered with Homer's fingerprints and loaded with bullets that match the one fired into Mr. Burns. Homer is accused of attempted murder and arrested. On the way to jail the paddywagon overturns at the Krusty Burger drive-thru due to Chief Wiggum unbalancing the weight as he leans out the window to collect his order, and Homer escapes.

At the hospital, it is revealed "Homer Simpson" is the only thing Burns can say, suggesting his "accusation" may not have actually been one. Hoping to clear Homer's name, Lisa returns to the scene of the crime to investigate and discovers the identity of Burns's true assailant. At the same time, Homer arrives at the hospital to confront his boss. After a police bulletin reports Homer's location, the police, Lisa, and many other citizens of Springfield race to the hospital. Upon entering Burns's room, everyone finds an enraged Homer vigorously shaking Burns. This returns Burns's ability to speak normally, and he quickly asks who the person shaking him is. Apoplectic with fury at Burns again not remembering who he is, Homer aims Wiggum's gun at Burns's face, demanding he recant his accusations. Burns laughs at the idea and confirms Homer did not shoot him. He then reveals the true assailant: Maggie.

After leaving the town meeting, Burns came across Maggie eating a lollipop in the Simpsons' car. He decided to try stealing candy from a baby, but Maggie would not let go of the lollipop, resulting in a struggle. As he finally yanked it away, his gun slipped from its holster into Maggie's hands and fired at Burns. The gun and lollipop both fell beneath the car seat; Homer would later unknowingly leave fingerprints on the gun while feeling around under the seat for an ice cream cone he accidentally dropped. Lisa guesses that with his last strength Burns pointed to the "S" and "W" on the sundial (with the "W" appearing as an "M" from his perspective) to identify his assailant. Burns corrects her, saying that with his last strength he swallowed his gold fillings to prevent the paramedics from stealing them, the positions of his arms being purely coincidental.

Burns demands for Maggie to be arrested, but he is dismissed by Wiggum, who says no jury would convict a baby for a crime. Marge also adds the shooting must have been an accident, considering Maggie, being an infant, is very unlikely to know how to operate a gun. In the final shot, Maggie is shown with shifty eyes as she sucks her pacifier in a way that sounds like gunshots, implying that she shot her father's boss intentionally.