Who shot Mr. Burns is the only two part episode of the entire Simpsons series.
At the beginning of the new school year, Principal Skinner opens up the school to find that Superdude, the 4th grade gerbil, has died. He gives Willie the task of burying the gerbil, and in the process Willie strikes oil. Everyone in the school rejoices, as now they have all the money they could ever want. Several teachers want new equipment, Willie wants a crystal slop bucket, and Lisa wants to hire Tito Puente to teach jazz at the school. However, Monty Burns has his eyes on the well, and wants to steal the oil (since Smithers forbid him from literally stealing candy from a baby.) First he tries to get Skinner to give the money to the Nuclear Plant by poorly disguising himself as Jimbo Jones, but to no avail. Finally, he uses a "slant drilling" operation to tap the well before the school can, thereby stealing the oil. The jet of oil smashes into Bart's treehouse, leaving it in a wreck and breaking Santa's Little Helper's legs. The drill also crushes the ground under Grampa's retirement home, and the fumes from the oil force Moe's Tavern to close. And of course, all the faculty and Lisa don't get their special equipment (and Tito Puente) because the school is now bankrupt from building the oil well. All of these people (and Homer, who flips out when Burns can't remember his name) swear revenge on the old man. Not even Smithers can stand the acts his beloved employer has undertaken, sarcastically saying that Burns has crushed all his enemies: An old folks home, the local tavern and Springfield Elementary. Burns says he hasn't taken out his biggest enemy: the sun. He plans to block out the sun, thereby forcing the town to use his electricity forever. Smithers say's he's stood by enough of Burns schemes but this one is too much and says he will have no part of it. Burns then fires him. Mayor Quimby calls a town meeting, after noticing that many in the audience are stroking guns, he opens the floor. Several people complain: Mr. Smithers tells everyone that since Mr. Burns fired him, he has become a drunk and always watches Comedy Central; Moe is mad that he lost his bar; Barney is mad that he lost Moe's bar; Lisa is mad that he robbed the school of music; Skinner is mad that he robbed the school of financial security; Tito is made that he "robbed the school of Tito"; Homer is mad that he can't remember his name; Marge is mad that he is making everyone yell; and Bart is mad that he broke Santa's Little Helper's. Mr. Burns then shows up, and Bart charges at him in rage. Mr. Burns brandishes a gun hiden in his jacket, stating that he has decided to protect himself ever since he was attacked in his office by an unidentified assailant (Homer, of course). Burns moves the machine into place, blocks out the sun, and as he leaves, it is noticed that many townspeople are missing. A gunshot is heard, and Mr. Burns staggers out of an alleyway, collapsing onto the sundial, shot. Marge then comments that they may never know who did this, since everyone in town is a suspect. After a long silence Dr Hibbert, with his trademark chuckle says "Well I couldn't possibly solve this mystery. Can YOU?" pointing at the screen, at what is thought to be the viewer.The camera zooms out to show that he is pointing to Chief Wiggum, who says he will give it a shot, since it is his job. An ominous tune plays after this. The words To Be Continued appear onscreen.
Mr. Burns is now hospitalized in a coma, and the Springfield police are working to find the assailant. Since their only witnesses are Maggie and Santa's Little Helper, their primary suspect is Smithers, who vaguely remembers shooting someone the night before. Guilt-ridden, Smithers heads for a local church, and is promptly arrested when the confessional turns out to be a police trap. While being interviewed by the media, Smithers makes a witty remark which Sideshow Mel realizes is from an episode of Pardon My Zinger that aired at the time of the shooting and that Smithers must have watched, giving him an alibi. It turns out that Smithers had actually shot Jasper's wooden leg; following this, Smithers is released from jail.
With one of the prime suspects cleared, the police, aided by Lisa, eliminate other suspects, including Tito Puente (whose revenge took the form of a "slanderous mambo"), Principal Skinner (who was busy applying his camo make-up at the time of the shooting), Groundskeeper Willie (who cannot fire a pistol due to his arthritis), and Moe (who is cleared and humiliated via polygraph test). After a surreal dream about Lisa, Wiggum finds an eyelash on Burns' suit which matches Simpson DNA. At the same time, Burns wakes up from his coma and cries, "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 arrested for attempted murder, but escapes from the paddywagon when it overturns. Smithers offers a reward for his capture.
At the hospital it is revealed that "Homer Simpson" are the only words that Burns can speak. Lisa returns to the scene of the crime to investigate and finally figures out the identity of Burns' true assailant. At the same time, Homer, disguised as a doctor, arrives at the hospital to silence Burns, who keeps saying his name. A police bulletin reports Homer's location, and Lisa, the police, and citizens of Springfield all race to the hospital. Upon entering Burns's room, everyone finds an enraged Homer shaking Mr. Burns vigorously. The shaking returns Burns's ability to speak normally, and he reveals the true assailant: Maggie Simpson.
Burns reveals what really happened on the night he was shot: after leaving the town meeting, he came across Maggie with a lollipop in the Simpsons' car. Burns decided to try stealing candy from a baby again but Maggie's strength proved comparable to his own due to his frailness, and there was a struggle for the lollipop. As he finally yanked it away, his gun slipped from its holster into Maggie's hands and fired. The gun and lollipop both then fell beneath the car seat; Homer would later unknowingly leave fingerprints on the gun while feeling around under the seat.
Burns demands that Maggie be arrested for the crime, but he is dismissed by everyone. Marge adds that the shooting must have been an accident. However, a final shot of Maggie's shifting eyes could suggest otherwise.
These are the 13 suspects that attempted to kill Mr. Burns due to his wrong doings against them.
- Homer - Mr. Burns purposely can't remember his name
- Skinner - Burns stole the oil Willie discovered underneath the school ground
- Willie - Burns stole the oil he found making him lose his job at the school and not get the expensive thing he wanted
- Moe - Loses his bar because of the fumes from the oil Mr. Burns stole from the school
- Barney - Lost Moe's bar for the same reason as Moe
- Grandpa - Lost his bed and home because of an aftershock caused by Burn's construction site
- Tito - Fired when Skinner sacrifices the music program due to Burns robbing the school's oil
- Bart - Burns hurts his dog
- Mr. Smithers - Burns fires him when he tried to persuade him from blocking the sun
- Apu and Dorris - upset with Burns for going too far with his evil schemes
- Sea Captain
- Sideshow Mel
These are the people who certainly could not have shot Mr. Burns.
- Marge - Gasps at Mr. Burns wounded
- Jimbo - Asks Mr. Burns are you okay
- Krusty - Away for six weeks
- Carl - Found that Mr. Smithers left his jacket behind at Town Hall
- Otto - Found that Skinner left his mother behind
- Ned - Wouldn't dare kill Burns