Smithers is convinced that he was the one who pulled the trigger while drunk, so he confesses to a priest who turns out to be a police officer, and he is arrested, then released when he recalls more. The Simpsons car is searched and the police find a gun covered with fingerprints, so Homer is made the prime suspect. He escapes from the prison van, and advances on Burns, who wakes up in the hospital and finally reveals the culprit's identity.
Waylon Smithers wakes up in his apartment and hears someone taking a shower in his bathroom. When Smithers opens the shower door, he finds Mr. Burns, alive. After Smithers decides the events of the previous night were a dream, Burns announces that the year is 1965 and that he and Smithers are undercover detectives on the Hotrod circuit, in some imaginary T.V series called Speedway Squad. Smithers wakes up again to find his detective work was a dream, his apartment is still a wreck, and that his mouth still tastes like an ashtray (which is quickly revealed that he was eating cigarette butts).
Kent Brockman reports on Mr. Burns assault. He was pronounced dead until transferred to a better hospital where doctors "upgraded" his condition to alive. After Brockman speaks to Chief Wiggum, it is revealed that two witnesses are already being questioned: Maggie and Santa's Little Helper, as they were both in the area when Burns was shot. Naturally, neither of them talk.
At the Simpson residence, Lisa says that everyone in Springfield had a reason for shooting Mr. Burns, even themselves. Everyone starts arguing amongst themselves about who did it, when Marge announces that there is already a prime suspect: Waylon Smithers. Smithers is already starting to wonder if he himself shot down Mr. Burns in a drunken rage. When he finds a recently fired gun in his jacket, he remembers that after he left the town meeting, he ran into some old man on the way home, and shot him. Smithers bursts into tears, crying, "What have I done?"
Moe, Barney, Lenny and Carl arrive at Homer's house and ask if he wants to come and help pull down Burns’ sun blocker. With the help of Snake, Otto, Groundskeeper Willie and the Bumblebee Man, they snap the machine in half. The sun blocker crashes into Shelbyville, much to everyone's delight. Smithers, meanwhile is driven mad by guilt and goes to a Catholic church and confess his sins. When he finishes, Chief Wiggum (who was in the confessional instead of a priest) emerges and takes Smithers in for questioning. Both the police and the press interrogate Smithers. At a press conference, Smithers cracks a Madonna gag to Kent Brockman. Krusty, who is watching the TV at the time, claims it was his joke, but Sideshow Mel says that Krusty stole it from an episode of Pardon My Zinger. Mel remembers that Smithers once said that he never missed an episode of that show, which airs on Comedy Central at 3pm, the very time Burns was shot. Mel heads for the station to point this out and Smithers recalls that he left the town meeting early to get home in time, and that the old man he ran into on the way was Jasper. The police and Smithers head for the newly repaired retirement home to check on Jasper and discover that Smithers did shoot him, but in the wooden leg.
With the prime suspect cleared, the police continue to investigate the matter. Lisa decides to help by making a chart of all the other major suspects. However, she forgets about Tito Puente, and when she tells the police (when Wiggum points out he's a suspect) that he did vow revenge, the police go to check him out. However, the kind of revenge Tito has in mind is an insulting, albeit catchy, tune; Tito is cleared. Skinner is next on the list, but the police clear him when he tells the police that he did go to the town meeting to ambush Burns, but he was in the lavatory applying his camouflage make-up at the time of the shooting. Superintendent Chalmers can vouch for Skinner's whereabouts as he entered the lavatory at the time of the assault too, just as Skinner realized he had taken his mother's make-up kit instead of his camo make-up (Skinner is quick to point out anything else Chalmers tells the police "is a filthy lie!").
The police questioned Willie next but he claimed it was impossible for him to fire a gun as he had crippling arthritis in his index fingers from playing Space Invaders in 1977. The police eliminated Moe as a suspect with the help of a lie detector, though Moe is utterly humiliated in the process.
At the Simpson house, Marge discovers that Grandpa's gun, which she buried in the backyard, is missing and asks Grandpa where it is. After he complains that people blame him for everything, Marge leaves. Grandpa removes the gun itself from his sweater, stroking it and telling it that he had missed it bad.
At the station, Wiggum prepares to pour some coffee, but after finding out he is out of coffee, he drinks some warm cream. He begins to dream, during which time Lisa tells him to check Burns' suit for more clues. While checking the suit, he finds an eyelash and tests it for DNA. Wiggum finds that the eyelash matches Simpson DNA. At the same time, Burns wakes up from his coma and cries, "Homer Simpson!"
The police raid the Simpson home for more information. A gun is found in under the seat of Homer's car. Homer claims he has never seen the gun before in his life, but his fingerprints are all over it. When Wiggum discovers that the bullets in the gun match the one they took out of Mr. Burns, he arrests Homer for attempted murder. After Homer is led into the police truck, Wiggum and the cops stop at Krusty Burger. Due to the trucks height, they are unable to enter the drive-thru. Wiggum decides to drive up the curb, which succeeds until Wiggum takes the food. The imbalance of the police officer's weight causes the truck to tip, damaging the back doors in the process. Homer seizes this chance and he escapes from the truck, heading for the hospital.
At the station, Waylon Smithers offers a $50,000 reward for Homer's capture, dead or alive. Lisa returns to the scene of the crime and, with the help of an intelligent pigeon, learns the identity of Burns' true assailant. At the hospital, Dr. Nick discovers some startling information as well. When Mr. Burns shouted "Homer Simpson!" he wasn't giving the name of his gunman, it was because "Homer Simpson" was all he could say. The doctor leaves, and Homer himself, who had successfully infiltrated the hospital and reached Burns' ward, prepares to silence Burns for telling everybody that Homer shot him.
A police bulletin reports that Homer has been spotted at the hospital. Lisa, the police, and the rest of Springfield race to the hospital. Lisa gets there first, protesting to everybody that her father wouldn't hurt a fly. On entering the ward, everyone finds Homer shaking Mr. Burns vigorously, telling him to stop telling everyone that Homer shot him. As Homer continues to shake him, Burns finds his voice and asks, "Smithers, who is this beast that's shaking me?" Homer yells at the top of his lungs,"D'oh!" snatches a gun from Wiggum and shouts at Burns to tell everyone that he never shot him. Mr. Burns laughs, stating that Homer doesn't have the cranial capacity nor the right amount of fingers to use a gun. And with that, Burns reveals his assailant to be Maggie Simpson.
Burns begins telling his story from the point where he left the town meeting. With the success of his sun-blocker, he had felt like celebrating. He walked into the parking lot to find Maggie, alone, in the Simpson car. She appeared to be smiling. He asked what she was so happy about, and she held up a lollipop. Homer pulls that very same sucker out of his shirt pocket; he had picked it up off the car floor when he was searching for an ice cream cone he had dropped. It was also there that he had absent-mindedly handled the gun, which explained why his fingerprints were all over it. Burns had tried to wrestle the candy away from Maggie, which was proving difficult. Eventually, his gun fell out of its holster into Maggie's hand and she fired it at him, although you can barely see her pull the trigger. The gun and lollipop then fell out of her hands underneath the car seat.
Mr. Burns, losing strength, tried to find aid, but finding only a useless Jimbo, he gave up and collapsed on the sundial, where he used his last ounce of strength to suck out his gold fillings and swallowed them so as to keep paramedics from stealing them. Mr.
Burns demands that Maggie be arrested, despite Marge's protests that the whole ordeal was an accident. Wiggum says that no jury in the world will convict a baby—except maybe Texas. Marge also adds that the shooting must have been an accident, but a final focus on Maggie's eyes suggests otherwise...
Allegedly to keep the ending from being leaked from animators and writers, there were actually several different conclusions created. Most were nothing more than footage of various characters shooting Burns, but there was also a full-length conclusion animated in which Smithers shot Burns and explained his doing so at Burns' bedside after Homer's wild chase. This footage was seen in "The Simpsons 138th Episode Spectacular." This was done to prevent the public from sussing out the real killer. As Troy McClure states in "The Simpsons 138th Episode Spectacular" the alternate ending wouldn't have made sense because for Smithers to have done it, all of the Simpson's DNA evidence would have to be ignored, which would "downright nutty", a reference to O.J. Simpson and his acquittal after the jury ignored the DNA evidence.
As revealed in the DVD commentaries for the episode, a number of subtle clues, and a few red herrings, were planted in Part 1 for viewers who wanted to unravel the mystery. For example, after Mr. Burns says "You all talk big, but who here has the guts to stop me?", the camera pans across the entire crowd. All the people look at Burns and then at each other, as if hoping that someone else will do the deed — all except one. The only person in the whole crowd who keeps her eyes fixed squarely on Burns is Maggie!
Also, when Burns was viewing the oil pump he said, "Oh Pish Posh, it'll be like taking candy from a baby." Burns was trying to take candy from Maggie when he got shot. Burns' "Oh, it's you" when he sees his assailant shows that he knew the person who shot him.
Much was made of the fact that Burns lay his hands on "W" and "S" on the sundial. It was assumed that these initials stood for the name of his assailant. When Burns receives chocolate from Homer, he talks about the family and says about Santa's Little Helper, "Oh there's that Simpson mutt." Grandpa's gun was a Smith & Wesson. SW could be reversed to mean WS, as in Waylon Smithers. SW flipped upside down makes MS, meaning Maggie Simpson, as Lisa points out in the end. When Mr. Burns was talking with Skinner in his office there was a diploma in the background that said "W. Seymour Skinner." Also, Moe's liquor license reads Moe Szyslak, his last name being revealed. Sideshow Mel is also present, but reveals his name to be "Melvin Van Horn." Also, there was a possibility of Marge Simpson.
It was suggested that the assailant was not Skinner, as he had a silencer on his gun, but the shot that wounded Burns could be heard clearly. Moe also had a shot gun which would have done much more damage to Burns, indicating that someone else shot him (although one of the "alternate endings" features Apu firing multiple shots at Mr. Burns with a submachine gun at point-blank range, with Mr. Burns receiving only a single gunshot wound). Also, it is worth noticing that Sideshow Mel couldn't have shot Mr. Burns - when everyone is threatening him (Mr. Burns), Sideshow Mel is wielding a knife, and a gunshot was heard at the time of the incident. Jimbo and Marge also have an alibi, for as Mr. Burns staggers towards the sundial at the end of Part 1, he passes both of them.
Smithers states that he never misses a program on Comedy Central that airs at 3pm on weekdays called Pardon My Zinger. Burns was shot at 3pm at Friday. Therefore, this proves that Smithers was not the gunman as also suspected by Sideshow Mel as well as going home drunk and shooting Jasper's artificial knee. Smithers also turns in the opposite direction to Burns after the town meeting. When Burns collapsed at the sundial, he does not have his gun with him, indicating that was what he is shot with.
Viewers were invited to participate in a contest to guess who shot Mr. Burns. The winner would be animated on an episode of the show. No one, however, was ever animated on the show.
This was because, as the DVD audio commentary for the episodes reveals, no one officially guessed the right answer. Due to contest regulations, a winner had to be selected out of a random sample of entries. Since the winner did not have the right answer, the commentary reports that the individual was paid a cash prize in lieu of being animated.
The creators and writers added on the commentary that they were aware of one person who posted the correct answer to the Simpsons newsgroup online after the night of the broadcast. They were forbidden from contacting the person while the contest was underway, but after it ended they wanted to contact the individual. The answer came from a person using a college internet account, and after the summer the person's address was no longer valid and they were unable to track the person down. They issued an invitation on the DVDs for this person to reveal him or herself.