Mr. Burns, being more evil than usual, brings untold misery to many of Springfield's citizens and is later found shot outside the city hall with the main suspects being Waylon Smithers, Jr. and Homer Simpson.
At the beginning of the normal ordinary school week, Principal Skinner opens up the school to find that Superdude, the 4th grade gerbil, has died. He gives Groundskeeper Willie the task of burying the gerbil, and in the process Willie strikes oil. Meanwhile, up on the roof, Principal Skinner and Superintendent Chalmers are inspecting what caused the explosion when a worker comes up and tells them they struck oil. He also holds up the corpse of Superdude. After thanking Superdude, he tosses the gerbil off the roof. 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, Charles Montgomery 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. After launching the oil, it causes some mayhem in the town. The jet of oil smashes into Bart's treehouse, leaving it in a wreck, injuring Bart 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, and some of the faculty (including Groundskeeper Willie) are laid off as a result of the same bankruptcy. All of these people (and Homer, who flips out when Burns can't remember his name one too many times) 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 is shocked pointing out all plant life will die and Owls will hoot constantly, he says 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 drunken wreck 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 mad 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 legs (although he initially said "look what he did to my best friend" which caused people to assume that Mr. Burns did something horrible to Milhouse until Bart clarified that he meant Santa's Little Helper). Mr. Burns then shows up, and Bart charges at him in rage. Mr. Burns brandishes a gun hidden 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. He then says,"D'oh!"). He taunts the townspeople for trying to intimidate him but not having the guts to follow through with their threats. Burns moves the machine into place, blocks out the sun, and as he leaves, Krusty returns from Reno, although he quickly leaves when he sees the townspeople glaring angrily (having missed out on Mr. Burns' vile behavior). Mr. Burns walks into an alleyway, obscured from view, and says: "Oh it's you, what are you so happy about? I see. I think you'd better drop it." He is then to heard to struggle with someone. Marge notices that many townspeople are missing when a gunshot is heard, and Mr. Burns staggers out of the fog, collapsing onto the sundial, wounded. Marge then comments that they may never know who did this, since everyone in town had a reason to hate him. 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.
The episode (and the second part) received positive reviews from critics and the writers of the book I Can't Believe It's a Bigger and Better Updated Unofficial Simpsons Guide, Warren Martyn and Adrian Wood, called it "A superb end to the season - and what's more, it's a genuine whodunnit. There's no cheating - all the clues are there." "Who Shot Mr. Burns?" ranked 25th in Entertainment Weekly's Top 25 Simpsons episodes' list, in 2003.