Remy is a highly intelligent and idealistic young rat with unusually acute senses of taste and smell, who dreams of becoming a chef like his idol, the late Auguste Gusteau. However, the rest of his colony, including his brother Emile and his father Django, are interested in food only for sustenance. One day, when the colony is forced to flee their home because of Remy and Emile’s wild encounter with the homeowner whose ceiling housed their colony, Remy is separated from the clan and eventually finds himself above the kitchen of Gusteau’s Restaurant in Paris.
When Remy observes a young garbage boy named Alfredo Linguini attempt to fix a soup he has spilled, he recognizes that Linguini is unintentionally ruining it and fixes his mistakes. Linguini catches him in the act, but does not reveal him to Skinner, Gusteau’s former sous-chef and new owner of the restaurant. Skinner confronts Linguini for tampering with the soup, but when the soup is accidentally served to a critic and proves to be a success, Colette Tatou, the staff’s only female chef, convinces Skinner to retain Linguini. Skinner spots Remy trying to escape, and orders Linguini to kill the rat, but Linguini decides to keep Remy instead.
When Linguini is ordered to replicate the soup, he is helped by Remy. Skinner, having tried the soup, decides to retain Linguini. Back in Linguini’s apartment the two learn to communicate and devise a plan: Remy hides under Linguini’s toque at the restaurant and guides his movements like a marionette by pulling on his hair. Skinner orders Colette to teach Linguini to be a cook.
Remy witnesses Skinner’s discovery that Linguini is Gusteau’s illegitimate son and rightful owner of the restaurant, and gives the evidence to Linguini, who forces Skinner out. The restaurant thrives as Remy’s recipes become popular, though as Linguini and Colette develop a relationship, Remy begins to feel left out. He reunites with Emile and the clan, but is rejected by Django over his admiration for humans.
The dour world-renowned food critic Anton Ego, whose negative review had indirectly led to Gusteau’s death, announces he will once again dine at the restaurant. After an argument with Linguini, Remy leads his clan to raid the restaurant’s pantries in revenge, but Linguini drives them out. Remy is captured by Skinner, who intends to use his talents to create a line of frozen food products, but is promptly freed by Django and Emile. Linguini apologizes to Remy, having been unable to cook without him, and reveals the truth to his staff, but they all leave, heartbroken and in disbelief. Colette returns after recalling Gusteau’s motto, “Anyone can cook.”
Impressed by Remy’s determination, Django and the clan offer to help, and cook under Remy’s direction while Linguini waits tables. Skinner attempts to interfere, but is bound, gagged, and banished from the restaurant. Remy creates a variation on ratatouille which reminds Ego of his mother’s cooking. Humbled and delighted by the dish, Ego asks to meet the chef, so Linguini and Colette wait until the other diners have left before introducing Remy. Ego is stunned and writes a glowing review, saying how he now understands Gusteau’s famous motto, and indirectly calling Remy “nothing less than the finest chef in France.”
Despite the review, the restaurant is shut down due to the presence of the rats, causing Ego to lose his job and credibility as a critic. However, he now funds and frequents a popular new bistro, La Ratatouille, run by Remy, Linguini, and Colette as the rat colony settles into their new home in the bistro’s attic.