The film starts in sepia-tinted Kansas in the early 1900s. Dorothy Gale lives with her dog Toto on the farm of her Aunt Em and Uncle Henry. .
One day, after school, Dorothy and Toto get in trouble with a cruel neighbor, Miss Almira Gulch, when Toto bites her. However, Dorothy's family and the farmhands are all too busy to pay attention to her, which made Sora and the others very cross and annoyed. Miss Gulch arrives with permission from the sheriff to have Toto euthanized. He is taken away, but escapes and returns to Dorothy; she then decides to run away from home with Toto, Sora and the whole team to escape Miss Gulch. They meet Professor Marvel, a phony fortune teller, who realizes Dorothy has run away and tricks her via his crystal ball into believing that her aunt is ill so that she and the others may return home. They all raced home as a powerful tornado develops. Unable to get into the storm cellar, they all seek safety in Dorothy's bedroom. A wind-blown window sash hits Dorothy's head and she falls unconscious on her bed. They all wake up to find the house spinning in the air, held aloft by the twister. In the storm outside the window she sees an elderly lady in a chair, several farm animals, two men rowing a boat, as well as Miss Gulch pedaling her bicycle, who transforms into a cackling witch flying on a broomstick.
The farm house crashes in Munchkinland in the world of Oz, where the film changes to Technicolor. Glinda, the Good Witch of the North, and the Munchkins, welcome her as a heroine because the damaged house has landed on and killed the Wicked Witch of the East, leaving only her feet exposed. Her sister, the Wicked Witch of the West, arrives to claim the magic ruby slippers worn on her sister's feet. Glinda transfers them off her feet to Dorothy's feet instead. The Witch of the West swears revenge on Dorothy and Toto for her sister's death. Glinda tells Dorothy to follow the yellow brick road to the Emerald City, where the Wizard of Oz might be able to help her get back home.
On her way to the Emerald City, Dorothy meets and befriends the Scarecrow who wants a brain, the Tinman who desires a heart, and the Cowardly Lion who is in need of courage. Dorothy invites each of them to accompany her. After encountering the Witch, who attempts to deter them from their destination, they finally reach the Emerald City. Inside, after being initially rejected, they are permitted to see the Wizard (appearing to them in the form of a large head surrounded by fire) who agrees to grant their wishes when they bring him the Witch of the West's broom.
On their quest to the Witch's castle, the group pass through the Haunted Forest while the Witch views their progress through a crystal ball. She then sends her flying monkeys to ambush the four and capture Dorothy and Toto. At the castle, the Witch fails to get the slippers off Dorothy due to a magical barrier, remembering that Dorothy must first be killed. Toto escapes and leads her friends to the castle. After defeating three Winkie Guards and stealing their uniforms, they march inside and free her, but the Witch and her guards trap them. The Scarecrow drops a chandelier onto the Winkies, the group is chased across the battlements, before being trapped on both sides. The Witch sets fire to the Scarecrow and Dorothy splashes a bucket of water onto the flames; the Witch, also hit by it, melts. The guards rejoice that she is dead and give Dorothy the charred broom in gratitude.
Back at the Emerald City, the Wizard refuses to grant their wishes. Toto, expose the "Wizard" as a normal middle-aged man who has been operating and controlling the wizard; he admits to being a humbug and a bad wizard. Nonetheless, he grants their wishes by giving the Scarecrow a diploma, the Lion a medal, and the Tin Man a heart-shaped watch, enough to convince them that what they sought had been achieved. He then prepares to get Dorothy, Roary, Theodore and their whole team home in his hot air balloon but Toto chases a cat, Dorothy and all our heroes follow, and it leaves without them. Glinda arrives and tells them that they can still return home by Dorothy tapping her heels together three times and repeating, "There's no place like home".
After bidding a tearful goodbye to their friends, Dorothy, Sora and the whole team return home, coming to consciousness on Dorothy's bed and the side of it surrounded by Dorothy's family, the farmhands, Professor Marvel, and Toto.
Rocksteady & Bebop are working with the Wicked Witch of the West in this film.