Harry Callahan, Inspector, SFPD, had foiled the Scorpio Killer, but had thrown his badge into a river in shame at the cowardice of the city. The city, however, has overlooked this incident in tacitly acknowledging being wrong in its handling of Scorpio, and Harry is reinstated. He thus continues to carry a trusty Smith & Wesson .44 Magnum revolver and continues to be a terror to perps in San Francisco.
But he may have some unwanted competition, for labor racketeer Carmine Ricca is aquitted in the murders of a labor foe and the man's family and watching TV coverage of the story is a motorcycle cop. Ricca, his lawyer, and two bodyguards are pulled over by a traffic cop, and when they reach for their licenses, the men are shot to death by the cop. Harry and his new partner, Earlington "Early" Smith, venture to the scene, but are asked to leave by Harry's newest adversary on the force, Lt. Neil Briggs, who had Harry "loaned" from Homicide to Stakeout because he despises his methods.
Harry and Early leave and find lunch at an airport snack shop run by a Bill McKenzie, a former buddy of Harry's from the force. Early, a comparatively wet-behind-the-ears youngster on the force, is grossed out when McKenzie talks about the Ricca killing and a case he worked on involving a gruesome axe murder, all the while Harry chows down on his burger as though nothing is untoward.
But a code signal for trouble comes, and Harry notices a group of concerned airport officials gathering around a small cul-de-sac. Harry investigates and finds that airport security is sweating out the hijacking of a jetliner; Harry flashes his badge and learns the hijackers want an overseas pilot, so Harry volunteers.
Harry gets aboard the plane and begins taxiing for takeoff, but when the copilot asks if he knows how to fly, he replies that he doesn't - which shocks the gunmen enough for Harry to disarm one and kill the other, and gives him opportunity to show up Lt. Briggs when he arrives at the scene.
Later he arrives at a target range near Oakland and encounters an old friend, traffic officer Charlie McCoy. McCoy has recently left his wife Carol, though it is clear he still holds her close to his heart, and is bitter over how his life has changed. Harry, concerned, suggests Charlie retire, but Charlie vows never to do so and instead "go out fighting."
In the target range Harry encounters four rookie traffic cops - John Davis, Philip Sweet, Donald "Red" Astrachan, and Michael Grimes, who practice incessently and are inseperable buddies from their days as Army Rangers. Harry chats with them for a few minutes and even lets Phil Sweet try his .44; he is impressed by Sweet's dexterity with the heavy revolver and with the four young policemen overall.
The next day a uniformed officer sneaks to the estate of a known gangster who is hosting a swimming party. The cop throws a satchel charge into the pool and machine-guns all the partygoers, then sneaks away with over 30 people dead and Lt. Briggs appearing on television at the sight vowing such crimes will be stopped. Harry is watching the newscast at the house of Carol McCoy, and she is glad that the ordeal of her divorce is now over; she then asks Harry why he's never hit on her, but her seduction is interrupted by the play of her rambunctious children, then by a phone call to Harry from Earlington Smith, who is part of a stakeout at a general store where possible robbery suspects have arrived. Harry thus is forced to cut short his dinner date with Carol and drive to the back entrance of the store, where through a two-way mirror he and a uniformed officer monitor as Early and two checkout associates attend to customers before a suspect at the magazine rack leaves and then returns with three "salty-looking dudes" who promptly produce shotguns and pistols. The group's leader slugs the store's eldest associate, orders him to find the store safe, and then orders Early to his knees - a fatal mistake for it gives Harry the opening to blast the punk through the mirror and a gun battle erupts where Early shoots another robber while a third gets away by car and a fourth is shot dead by Harry. After the incident Harry and Early return to headquarters to finish the ensuing paperwork and Early encounters the four rookie cops, whom Early knows from their days at the police academy.
Later that night a pimp kills one of his girls, and is stopped the next morning and shot dead by the vigilante cop. Harry returns home that night where a new neighbor, a young woman named Sunny, greets him; a long-time admirer of his heroism, Sunny offers Harry her own gratitude by asking to bed him. But they are interrupted when Lt. Briggs calls Harry to the city morgue to view the bodies of victims of the vigilante, all of them known criminals. Harry is reassigned to Homicide by his and Briggs' superior, Captain Avery, but a clue is difficult to come by - there are no witnesses to the murders though uniformed patrolmen keep finding the bodies, and ballistics checks of the slugs reveal uselessly generic information about the weapons used.
The next day - after Harry and Sunny consummate her reward of gratitude - Harry and Early examine a bullet that proves to be a .357 Magnum round, and Harry begins to suspect that the killer of these criminals is someone they'd never suspect; he thus begins to clash with Briggs when Briggs suspects harborside racketeer Frank Palancio, who had worked with Ricca in the past, may be behind the murders.
Harry and Early tail Palancio and harass him as he is driven around the city. But elsewhere, the vigilante cop reaches the top of a penthouse and guns down Palancio associate Lou Guzman, who is being monitored by Harry's friend Frank DiGeorgio and his partner from an office building a block away. As the killer makes his way to the basement, he runs into traffic cop Charlie McCoy. McCoy seems to recognize the killer cop and thinks he is just another fellow officer - until the killer shoots McCoy, then upon seeing DiGeorgio tells them of McCoy's shooting, then keeps a crowd of bystanders back. The killer cop removes his helmet - revealing himself as John Davis.
Lt. Briggs chews out Harry for harassing Palancio before revealing McCoy's death. Harry and Davis see Charlie's widow and her kids off for the funeral flight back east, and Harry thanks Davis for showing his support. But Harry harbors suspicions about Davis; when they stumble into a robbery attempt at a bowling alley they subdue the robbers before Davis furiously dresses down bystanders for letting such crimes take place.
Later, Davis and Harry compete in a police shooting contest, and that night Harry finds and examines a bullet from Davis' gun, and it matches a bullet from Charlie McCoy's body. But Harry is reluctant to reveal all he knows when he shows Lt. Briggs a bullet under a forensic microscope, as he now trusts no one.
His mistrust proves warranted when a police raid hits Palancio's harborside offices. Harry has asked for John Davis and Phil Sweet to back him up, but the thugs (who had received an anonymous call that men dressed as cops would attack them in minutes) open fire, killing Sweet, and a gun battle ensues that leaves Palancio and his associates dead and Harry injured. When Briggs and Captain Avery try to blame Harry for the debacle, Harry fights back by noting Palancio's men fired first, indicating they were tipped off. Briggs refuses to believe it, vows to ruin Callahan's career, and has Harry hand over the bullet he showed earlier.
But the bullet is a fake, as Harry still has the one he found earlier. He now reveals all to Early Smith as he gives him the bullet to give to Briggs if anything happens to Harry. Harry, however, is confronted by the vigilante cops in the garage of his apartment, and when he finds a bomb in his mailbox - and must stop Sunny from accidentally detonating it - he discovers who the vigilante squad's ringleader is - but may not survive to expose him as the vigilantes go after him and a dangerous pursuit ensues.