Dorothy, Aunt Em, Uncle Henry, and their three farmhands are still cleaning up after the twister when they find themselves on the verge of losing what is left of the family farm, when neighboring Mr. Bibb files a lawsuit claiming that the twister released some of the Gale pigs who then plundered his prize watermelon patch. He takes the animals away unless Aunt Em, Uncle Henry and their farmhands can get jobs to get the money to keep their farm animals in twenty-four hours. Dorothy wants to help, but to her dismay, they tell her that she's too young. While her family is out looking for jobs, Dorothy, Tom, and Jerry stay at the farm to clean up the mess. However, they find themselves with a second problem: to their horror, one of the flying monkeys has come to attack. During the attack, Scarecrow, Tin Man, and Lion show up at Dorothy's farm. They tell Dorothy that Ruggedo the Nome King has taken over the Emerald City, captured Glinda and Tuffy and taken her wand, and now he wants to destroy Dorothy and seize her ruby slippers. Since his great fear of the Wizard has kept him underground, Dorothy and her friends journey to Topeka to get the Wizard to return to Oz and set everything straight.
After using some of Glinda's magic potion to bring the Gale farm tractor to life to take them to the Kansas State Fair, they are able to gain entry when they present the carnie at the gate with emeralds from the Emerald City to cover their entrance fee. Once they find the Wizard, he's grown tired of his magic shows and agrees to take them back to Oz in his hot air balloon, but needs the aid of another tornado to do so. Luckily, he keeps a bottle of magic tornado with him, and with the aid of a device one of the farmhands built to counter tornadoes in the future, they use it to travel back to Oz, but not without causing some damage to the State Fair in the process.
Once in Oz, they are attacked by the flying monkeys again, but Dorothy and the others have to separate from the Wizard when his balloon ends up getting several flying monkeys glued to it with one of his inventions and leave him to fend for himself. As they try to make it to the Emerald City on their own, they are attacked by the Jitterbug, whom Ruggedo released to slow them down, then are separated further when attacked by Ruggedo's Nomes, who capture Dorothy and the Scarecrow, while the Tin Man is thrown into the river, and Toto, Tom, and the Lion nearly fall into a chasm. Jerry rescues the Tin Man with aid from the Mouse Queen and her soldiers, while the Lion takes Tom and Toto into the woods on the long route to the Emerald City since they were separated from Jerry and the Tin Man. Meanwhile, the Scarecrow and Dorothy are able to escape Ruggedo's Nomes, reach the Emerald City, and attempt to see if there's anything in the Wizard's old chambers that can help them, but are captured by Ruggedo.
As for Tom, Toto, and the Lion, they soon end up at the Lion's old castle, where it seems he's been replaced as the leader of the forest by a very hungry female tiger. Though in the end, Toto seems to get the Lion and Tiger to cooperate and use their troops to aid Dorothy.
Back with Dorothy and the Scarecrow, Dorothy willingly surrenders the ruby slippers to Ruggedo, who transforms them into boots that enable him to plunge the Emerald City into the gnomes' underground home before considering putting Dorothy and the Scarecrow into a bottomless pit. Before he can, he is surprised by Jerry, the Tin Man, Tuffy, whom Ruggedo kicked out earlier, the Mouse Queen and her troops, and soon after, the Lion, Tom, Toto, the Tiger and her forces. Though he is disarmed of Glinda's wand, he overpowers all of them via the ruby slippers, and nearly sends Dorothy, Tom, Jerry, Toto, Scarecrow, Tin Man, and Lion to their doom, before the Jitterbug, whom Dorothy convinced to ally with them earlier, is able to trap Ruggedo in his dance spell, along with animating a statue of Dorothy that rescues everyone.
Tuffy, the Mouse Queen, and her troops use Glinda's wand to free her from her imprisonment, while Ruggedo is stripped of the ruby slippers when Tom and Jerry try to save him from falling into the bottomless pit and fail, leaving him to plunge to his doom. Once Dorothy puts them back on, she returns the Emerald City to the surface, and the Wizard arrives shortly thereafter, having managed to tame the flying monkeys that got glued to his balloon with one of his magic potions that made giant bananas for them.
With Oz safe once more, the Wizard returns to a formal position in the Emerald City while still leaving the Scarecrow, Tin Man, and Lion in charge, and after he and Glinda offer some final words of wisdom to Dorothy and how she is always welcome in Oz again whenever she wants to return, Dorothy takes Toto, Tom, and Jerry back to Kansas. Once home, they use the potion the Wizard gave them to help pay off Mr. Bibb and have him cancel his lawsuit against the Gale farm. When Uncle Henry, Aunt Em, and the farmhands return with little success in town, Dorothy reveals her success in saving their animals and farm, impressing them enough to realize she is old enough to handle things on her own. While Tom and Jerry get into their old antics again, Dorothy is happy to know that no matter what happens, there's no place like home.