Barry B. Benson (Jerry Seinfeld) is "just an ordinary bee" in a hive in Sheep Meadow, Central Park in New York City. Barry recently graduated from college and is about to enter the hive's Honex Industries (a division of Honesco Corporation and owned by the Hexagon Group) honey-making workforce. With his best friend Adam Flayman (Matthew Broderick), Barry is initially very excited, but his latent, non-conformist attitude emerges upon finding out that his choice of job will never change once picked. This prompts Barry to leave the hive and see the world on a daily run with the macho, elite "Pollen Jocks", though Adam tries to talk Barry out of it. He thoroughly enjoys his new freedom, and is impressed by the process of nectar collection and pollination, but after being stuck to a tennis ball during a game and flying through a panicking family's car he decides humans are crazy and that he should go home. Unfortunately, it begins to rain and he crash lands on a windowsill. The apartment's occupants, the same couple who hit Barry with the tennis ball, have just come home and they close the window before Barry can escape. After freaking out the people inside and nearly being squashed, he is rescued by a florist named Vanessa Bloome (Renée Zellweger) and gently put back outside. This unexpected act of kindness intrigues Barry, who goes back in to thank the woman even though doing so violates Bee Law #1, "Don't talk to humans". Against both of their expectations, they develop an instant bond, bordering on attraction, and start hanging out together frequently. Of course, all of their friends and family are upset by this relationship.
While they are going through a grocery store, Barry is shocked to discover that the humans have been stealing and eating the bees' honey for centuries and decides to journey to Honey Farms, which supplies the grocery store with its honey. On the Honey Farms truck, he meets a mosquito named Mooseblood (Chris Rock). A windshield wiper flings the two in a tube and Barry tells Mooseblood about Honey Farms while Mooseblood tells him about how humans have always swatted mosquitoes. Mooseblood departs when he sees a Blood Mobile pass by, while Barry goes on to witness the artificial process by which the honey is gathered. He ultimately realizes that his true calling in life is to set the world right by suing the human race for stealing their precious honey. This is later shown on Hive at Five's especially on Bee Larry King starring a bee version of Larry King. The trial initially goes well, until the defense lawyer, Layton Montgomery (John Goodman), accuses Barry of several things which are insulting to the bees (having a pet-like relationship with Vanessa, being an illegitimate son, since all bees are sons of the queen bee, and having incestuous flirtings with the female bees, since all bees are siblings) to show the less-lovable side of bees. This goads Adam to sting him, endangering his life. Barry counters by producing the smoke-machine used by Honey Farms to drug and subdue their bees. Adam is sent to the hospital, and is hooked to honey through I.V. His stinger is replaced with a pirate sword toothpick, and it turns out he is going to be fine.
Barry wins the lawsuit, and all honey in the world is confiscated and returned to the bees. However, Montgomery warns them they are disrupting nature's balance meaning that the bees quit their jobs. Adam comments to Vanessa that it might be true since bees had been living their previous lives over 27 million years. However it is too late, as Barry and Vanessa realize that the others were right. The sudden, massive stockpile of honey has put every bee out of a job, including the vitally important Pollen Jocks. Without bees pollinating the flowers, all plant life begins dying with the entire food chain close behind. To set things right, he and Vanessa find a way to save all the flowers by going to the Tournament of Roses Parade in Pasadena, California and bringing back with them all the pollen-filled flowers to re-pollinate the world. Barry and Vanessa fly the flowers as luggage on a flight from Los Angeles International Airport to John F. Kennedy International Airport. The flight begins to take a detour due to lightning, and the delay would be fatal to the flowers. Trying to intervene, Barry accidentally knocks out the terrified pilots. Vanessa joins him and tries unsuccessfully to fly the plane. In the meantime, millions of bees have rallied and arrive at the last minute to help them safely land.
Armed with the pollen of the last flowers, Barry and the Pollen Jocks manage to reverse the damage and save the world's flowers, restarting the bees' beloved honey production. Nothing is mentioned about the fate of companies like Honey Farms, though humans and bees are seen treating each other visibly better, and honey is supposed to be "bee approved". Barry becomes a member of the Pollen Jocks while Adam is working as a krelman, helping to pollinate the plants while running a law firm inside Vanessa's flower shop, as well as helping Vanessa, switching the name from "Vanessa's Flowers" to "Vanessa & co: Flowers, Honey, Music, and Legal Advice". As the film closes, his office door reads "Insects at Law". Mooseblood works in his office with him as a lawyer (stating that he is already a bloodsucking parasite and only needed a briefcase), which is shown when Barry is interviewing a cow about the human exploitation of her milk.