In Paris 1910, cat Duchess and her three kittens, Marie, Berlioz, and Toulouse, live with their owner, former opera star Madame Adelaide Bonfamille, and her butler, Edgar. One day, Edgar overhears Madame preparing her will with her lawyer. Edgar learns that Madame intends to leave her fortune to her cats until their deaths, afterwards passing it onto to Edgar. Edgar believes this is unreasonable and wants the cats to disappear. He sedates the cats and drives them out into the country to abandon them. Meanwhile, Madame and the cats’ other animal friends discover their disappearance.
Upon waking up in the country, Duchess meets an alley cat named Thomas O’Malley. He offers to help guide Duchess and her kittens back to Paris. They hitch a ride in the back of a milk truck but are discovered by the driver. They continue on foot. Trouble arises when crossing a river via a railroad bridge, they narrowly avoid an oncoming train and Marie falls into the river. O’Malley saves her, but he has to rescued by two geese who decide to accompany the cats to Paris. Edgar returns to the country to retrieve his possessions lost during his escape from two hound dogs, fearing that they will become evidence against him.
The cats return to Paris, travelling across the rooftops of the city. They meet O’Malley’s friend Scat Cat and his alley cat musicians, who perform the song Ev’rybody Wants to Be a Cat. After the band has finishes for the night, Duchess tucks the kittens into bed. O’Malley and Duchess converse on a nearby rooftop, and the kittens eavesdrop from the windowsill. O’Malley, having fallen in love with Duchess, proposes to her. Duchess declines due to her loyalty and love for Madame.
The next morning, Duchess and the kittens return to Madame’s mansion, but Edgar catches them and prepares to ship them to Timbuktu. The cats communicate to their animals friends to find O’Malley, certain he can help them escape. O’Malley returns to the mansion with his fellow alley cats. Together, they fight Edgar and free the cats from the wooden crate. The animals lock Edgar in his own packing-case and he is sent Timbuktu himself. Upon discovering his absence, Madame Adelaide’s rewrites her will to exclude Edgar, though she is unsure of his reasons for his sudden leave. She adopts O’Malley into the family and establishes a charity to house Paris’s stray cats.