The film begins showing wizard Kaldorf expelling a powerful witch named Drizelda from a village for multiple crimes. Kaldorf allows Drizelda's mistreated niece Athena to stay. The elf villagers fear she will turn out like her aunt because she keeps vermin (Jerry) and has an affection for cats (Tom). The cat and mouse in this timeline are babies and become frenemies to each other but friends with Athena, who is only a teenage barefoot girl.
The film fast forwards to Tom and Jerry chasing each other, as they usually do, and Athena caring for hurt animals, until the three happen to come across a mysterious glowing egg. What neither of them know is that this egg was stolen from a very large, fire-breathing dragon. In a short time, a baby dragon named Puffy hatches from this egg and believes that Tom is his mother, and the three take good care of him.
However, Puffy's real mother is angered that her baby is missing and wants him back, but before Tom, Jerry and Athena can even try to find her, Drizelda returns and captures Puffy, intending to use him for her own wicked plans — she is trying to steal his heat to become a super-dragon herself and destroy everything in the village. With the help of powerful allies and animal friends, Tom, Jerry and Athena work together and fight tooth and claw to stop the evil witch and get Puffy back to his mother, eventually, Drizelda is turned into a statue, and the villagers, Jerry, Kaldorf and even Athena are having a happy singing party, while Tom is chased by Athena's pet crocodile.
After the end credits, despite being turned into a statue, Drizelda is shown to still be alive. As a bird tries to perch on her, she breathes a puff a smoke from her nose, replying "Don't even think about it!", scaring away the bird.
