In June 1969, a family, including a five year-old girl named Jo, seek shelter in a storm cellar as a powerful F5 tornado strikes. The storm is so strong that the storm cellar door is ripped off and Jo's father is killed. Jo, her mother, and her dog Toby survive.
In the present day, Jo (Hunt), a meteorologist, is reunited with her estranged husband, Bill Harding (Paxton), a former weather researcher and storm chaser, who has since become a weather reporter. He is planning to marry sex therapist Melissa Reeves (Gertz), and needs Jo's signature on the divorce papers. Jo has built four identical tornado research devices called DOROTHY, based on Bill's designs. The device is designed to release hundreds of sensors into the center of a tornado to study its structure from the inside, with the purpose of creating a more advanced storm warning system. Bill and Melissa join Jo and her team of storm chasers, and the team encounters Dr. Jonas Miller (Elwes), a smug meteorologist and storm chaser. When Bill discovers that Jonas has created a device based on DOROTHY, called DOT-3, he vows to help Jo deploy DOROTHY before Miller can claim credit for the idea.
During the first tornado, Jo's truck and DOROTHY I are both destroyed. They continue chasing in Bill's truck, with Melissa in the back seat. They find a second tornado, a confirmed F2, and head off on a back road when it shifts its track. They soon find themselves driving through heavy rain and Bill's truck is spun around until the tornadoes dissipate.
The team visits Jo's aunt Meg's house in Wakita, Oklahoma for food and rest. They soon learn that a "hopping" F3 tornado is on the ground, but they have trouble finding it. Jo drives ahead of the team to intercept the oncoming tornado, but a telephone pole falls on the back of Bill's truck and knocks DOROTHY II out onto the road, disabling it. As the tornado lifts and touches down closer, Bill pulls Jo into the truck and moves to safety. The two confront each other over their marriage and Jo's obsession with stopping tornadoes, due to her father's death.
That following night, an F4 tornado devastates a drive-in cinema, forcing everyone to take shelter in a nearby warehouse. Melissa is traumatized by the experience, and leaves, recognizing the unresolved feelings between Jo and Bill. The tornado hits Wakita, devastating the town and injuring Meg while destroying her house. After Bill and Jo rescue Meg from her collapsing house, they hear that an even stronger storm, an F5, is forming 25 miles south of their position. Inspecting Meg's wind chime sculptures, Jo realizes that the most likely method to successfully deploy DOROTHY's sensors into a tornado would be to add additional body surface to catch the wind.
As they reach the F5, the team adds aluminum to work as wind flaps, but the deployment of DOROTHY III is a failure. Meanwhile, Jonas attempts to deploy DOT-3, but after ignoring warnings from Bill, his truck is caught by the tornado and he and his driver are killed. Jo and Bill set out on their own and are able to deploy the last DOROTHY successfully. Their celebration is cut short, however, as the tornado shifts course towards them. They take shelter in a shed where they anchor themselves to irrigation pipes. The tornado destroys the shed and Jo and Bill find themselves in the vortex of the massive funnel.
After the F5 dies out, Jo and Bill find themselves alone on the floor of the former shed. They then decide to run their own lab and rekindle their marriage.
That following night, an F4 tornado devastates a drive-in cinema, forcing everyone to take shelter in a nearby warehouse. Melissa is traumatized by the experience, and leaves, recognizing the unresolved feelings between Jo and Bill. The tornado hits Wakita, devastating the town and injuring Meg while destroying her house. After Bill and Jo rescue Meg from her collapsing house, they hear that an even stronger storm, an F5, is forming 25 miles south of their position. Inspecting Meg's wind chime sculptures, Jo realizes that the most likely method to successfully deploy DOROTHY's sensors into a tornado would be to add additional body surface to catch the wind.
As they reach the F5, the team adds aluminum to work as wind flaps, but the deployment of DOROTHY III is a failure. Meanwhile, Jonas attempts to deploy DOT-3, but after ignoring warnings from Bill, his truck is caught by the tornado and he and his driver are killed. Jo and Bill set out on their own and are able to deploy the last DOROTHY successfully. Their celebration is cut short, however, as the tornado shifts course towards them. They take shelter in a shed where they anchor themselves to irrigation pipes. The tornado destroys the shed and Jo and Bill find themselves in the vortex of the massive funnel.
After the F5 dies out, Jo and Bill find themselves alone on the floor of the former shed. They then decide to run their own lab and rekindle their marriage.
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