After witnessing gangster Eddie Kim (Byron Lawson) commit a murder in Hawaii, Sean Jones (Nathan Phillips) is escorted by FBI agents Neville Flynn (Samuel L. Jackson) and John Sanders (Mark Houghton) on a Boeing 747-400 to testify in a trial in Los Angeles. Despite increased security for the flight, Kim arranges for a time-release crate full of venomous snakes to be placed in the cargo hold in an attempt to bring down the plane before it reaches Los Angeles International Airport (LAX). To ensure the snakes attack the passengers without being provoked, he has one of his henchmen spray the passengers' leis with a special attack pheromone.
The crate opens midway through the flight, and the snakes make their way through the cabin. A couple having sex in the bathrooms are the first killed. The plane's captain, Sam McKeon, investigates and fixes an electrical short, but is killed by the viper that caused it. Co-pilot Rick (David Koechner), unaware of the snake, believes Sam has suffered a heart attack and continues on to LAX. Some of the snakes then attack Rick, and while fending them off, he accidentally releases the oxygen masks throughout the plane, and snakes drop into the cabin with them. Numerous passengers, including Agent Sanders, are killed. The surviving passengers, who have made their way to the front of the plane, put up blockades of luggage to stop the snakes. A young boy gets bitten by a cobra, but an American Cajun woman (Elsa Pataky) traveling with her baby is able to suck out most of the venom. Meanwhile a socialite named Mercedes (Rachel Blanchard) is distraught when a passenger feeds her pet chihuahua to an anaconda.
Agent Flynn contacts FBI Special Agent Hank Harris (Bobby Cannavale) on the ground who gets in touch with ophiologist Dr. Steven Price (Todd Louiso). With pictures of the reptiles emailed to him via a mobile phone, Price believes a Los Angeles snake dealer to be responsible. After a shootout with the dealer, he reveals that he obtained the snakes for Kim. His supply of antivenom is commandeered for the plane's surviving snakebite victims, and Harris orders Kim's arrest.
Rick is attacked by the viper that killed Sam and the plane starts to dip downwards, causing a food trolley to crash through the luggage blockade. Many passengers flee to the upstairs first class cabin. The passengers block the cabin's entrance with an inflatable liferaft. Agent Flynn and Flight Attendant Claire (Julianna Margulies) manage to regain control of the plane after a struggle with the yokes. Rick retakes the controls and has Flynn go into the cargo hold in order to restore the air conditioning/ventilation system.
Harris then contacts Flynn telling him that antivenom will be ready for the passengers when they land. However, Flynn discovers that the cockpit is filled with snakes and that Rick is dead. After a brief discussion, Troy (Kenan Thompson), bodyguard to rapper Three Gs (Flex Alexander), agrees to land the plane based on prior experience. After everybody gets prepared, Flynn shoots out two windows with a pistol, causing the plane to depressurize. The snakes are blown out of the cockpit and the lower floor of the plane.
Flynn and Troy take the controls of the plane and Troy reveals that his only flight experience was from a video game flight simulator. After an emergency landing, the plane makes it safely to the terminal. The surviving passengers leave the plane, and antivenom is given to those who need it. Just as Flynn and Sean are about to disembark the plane, a snake jumps out and bites Sean in the chest. Flynn draws his gun and shoots the snake, and paramedics rush to Sean, who is unharmed due to a bulletproof vest. Sean later takes Flynn to Bali and teaches him how to surf.