Glamorous, beautiful and apparently independently wealthy Melanie Daniels has one of those “meet cutes” more common to romantic comedies than suspense thrillers when she stops into a pet shop in San Francisco. The other side of this romantic equation is Mitch Brenner. Mitch is a young lawyer who comes into the pet shop for the purpose of buying a pair of lovebirds to take home to his little sister Cathy, but he recognizes Melanie and tricks her into thinking that he believes she works there, so he can make a joke at her expense.
After Mitch leaves without any lovebirds, Melanie is simultaneously frustrated by his mocking and charmed by him. She decides to purchase the pair of lovebirds herself and take them to Mitch’s apartment, finding out the address by using her connections to a large San Francisco newspaper, which her father owns. When she finds out that Mitch has gone home for the weekend, she decides to take the birds all the way to the Brenner home in Bodega Bay, 60 miles north along the coast. She finds out Mitch’s younger sister’s name (Cathy) from the schoolteacher, Annie, who seems to have a history with Mitch. She sneaks up to the Brenner house on a boat from across the bay, breaks in, and leaves the birds and a note for Cathy. On the way back across the bay in a small motorized boat, a seagull suddenly dives toward Melanie’s head, giving her a bloody gash before soaring out of sight.
Mitch is waiting for her on the pier and decides to invite her back to his home after helping her tend to her injury. His mother comes into the restaurant during this scene and is immediately suspicious of Melanie; it's clear that she is overprotective of her son. At dinner with the family, we find out that there is something wrong with Brenners’ chickens. Later that night, a gull crashes into the door of Annie’s house, where Melanie is staying, as if it were trying to get inside. We also find out that Annie and Mitch used to date quite seriously, but Annie was chased away by Mitch’s mother, Lydia. Tension between Lydia, Melanie, and Annie will continue for the rest of the film, though it subsides in the face of the bird attacks.
The next day at Cathy’s birthday party, the children are attacked by a group of gulls. Annie, Mitch, and Melanie come together to save the children, and the only injury sustained is a single scratch down a girls cheek. Later that night, hundreds of sparrows seem to intentionally come down the chimney inside the Brenner home, terrorizing the family and Melanie (who has stayed for dinner). They escape unharmed and the local policeman, Al Malone, comes to inspect the scene but offers no satisfactory explanations or courses of action. Melanie stays over at the Brenner house after the attacks because she is scared to go back home.
The following morning, things seem normal until Lydia arrives at the Fawcett farm, where Dan Fawcett has also been having trouble with his chickens. She enters the house to find Dan dead in his bedroom with the windows broken, dead birds everywhere, and his eyes pecked out. She hurries home in shock, where Melanie and Mitch take care of her. Mitch goes to the Fawcett Farm to help Al analyze the scene, and Lydia and Melanie begin to bond—it seems as though Lydia’s fear, coupled with Melanie’s kindness have allowed Lydia to become more open with Melanie. Lydia then sends Melanie to the school to fetch Cathy, because she is worried about her safety.
At the school, Melanie waits outside for class to end, but eventually notices that hundreds of crows have ominously gathered behind her. She rushes inside and tells Annie, because she is worried that the birds will break in through the windows and harm the students. Annie calls a fire drill so the class will leave, and as they exit the school and begin running down the hill, the crows attack. Several children are injured, including one of Cathy’s friends, who is knocked on the ground.
By now, it has become clear that the town is under some sort of attack by birds, although a local ornithologist argues strongly against reading any intent into the attack. In the main restaurant at the center of town, several townspeople argue with Melanie and the ornithologist about the attacks. A mother with her two children overhears and becomes incredibly frightened, and tries to leave for San Francisco. However, another attack starts just as she is leaving. The birds cause an explosion at the local gas station by attacking a man who is pumping his car, which leads to a massive, swarming assault upon the town, in which at least one person is killed. Melanie seeks refuge in a phone booth and is rescued by Mitch. When they finally make their way back to the diner, Melanie is accused by the frightened mother of somehow being responsible for the attacks since they coincided with her arrival on the island. Mitch and Melanie then go to Annie’s home to find Cathy safe inside, but Annie dead on her front steps.
Mitch boards up all areas of entry at their house, preparing for another attack. The attack eventually starts and an endless torrent of birds attack the house while Mitch struggles to keep them at bay. By the middle of the night the attacks subside. A little while later, however, Melanie hears fluttering above her while the others sleep. She makes her way upstairs and gets trapped inside a bedroom with a giant group of birds that broke a hole in the ceiling to get in. They attack her and she is severely injured, but Mitch and Lydia are finally able to rescue her. She seems to be inching closer to madness after being at the center of four different bird attacks, is overcome with fear, and simply stares blankly for much of the rest of the film. Mitch decides it is time to time try to make it to their car in order to get to San Francisco and—hopefully—safety. As Mitch starts the car, he hears on the radio that there have been more attacks in towns nearby.
As the Brenners’ and Melanie exit the house, hundreds of birds eerily stand by watching them without attacking, allowing them to make it to the car safely. They take Cathy’s lovebirds with them. As they slowly drive away, thousands or perhaps even millions of birds sit perched and watching, and it is unclear if more attacks will come or if the characters will finally be safe in San Francisco.