Now serving as Paris’ Captain of the Guard under the new Minister of Justice, after the death of the previous one (Judge Claude Frollo), Captain Phoebus and Esmeralda have married and have a six-year-old son named Zephyr. Quasimodo is now an accepted part of Parisian society; though he still lives in Notre Dame with his gargoyle friends Victor, Hugo, and Laverne, and still serves as the cathedral’s bell-ringer.
A circus troupe led by Sarousch enters town as part of “Le Jour d’Amour”, a day dedicated to the celebration of strong and pure romantic love and romance (in a fashion similar to Valentine’s Day). However, it is revealed that Sarousch is, in reality, a master criminal who plans to steal Notre Dame’s most beloved bell, La Fidele (“the faithful one”; a take on the real-life Notre Dame’s biggest bell, the Emmanuel), the inside of which is decorated with gold and enormous jewels. He sends Madellaine, his aspiring assistant, to discover the whereabouts of La Fidele. She encounters Quasimodo without seeing his face, and the two of them seem to get along quite well despite having just met, but she runs away after seeing his face, shocked at his deformed appearance. The gargoyles convince Quasimodo to go to the circus to see her again. Sarousch captures the audience’s attention by making an elephant disappear, while his associates steal from the audience. Sarousch forces Madellaine to follow Quasimodo and obtain the information he wants. At first she tries to persuade Sarousch not to do so, but he reminds her of her background: years ago, when Madellaine was only a six-year-old girl, Sarousch caught her trying to steal coins from him, but instead of turning her over to the cruel Frollo, Sarousch took her under his wing out of sympathy. She follows Quasimodo and Zephyr, and sees them spend the afternoon playing together. Eventually, the exhausted Zephyr falls asleep in Quasi’s arms. Realizing that Quasimodo possesses a kind and gentle nature, Madellaine ceases to be frightened by his appearance. Quasimodo takes her around Paris, and shows her numerous sights.
Later, while Quasimodo is out with Madellaine, Sarousch and two of his subordinates sneak into the cathedral. Zephyr and Djali the goat follow them and watch as Sarousch causes La Fidele to vanish. The gargoyles, who had tried to drop a bell on the thieves, end up trapped under it; Laverne rams one of its sides, causing the bell to clang loudly. Hearing the sound, Quasimodo and Madellaine rush back. When the Archdeacon informs everyone that La Fidele has been stolen, Clopin claims that if they do not find the bell, the festival will be ruined. Phoebus suddenly realizes that Sarousch was behind the whole thing and played him for a fool. He sends the soldiers all over Paris to find Sarousch. Realizing now that Madellaine has deceived him (despite her pleas that she didn’t intend to), Quasimodo angrily breaks off the relationship and tells Phoebus that he was right before running off into the cathedral, feeling heartbroken and betrayed. Feeling sorry for Quasimodo, Phoebus has the guards arrest Madellaine for her involvement in the theft.
Sarousch and his men attempt to escape with the bell through the catacombs, taking Zephyr as hostage. Phoebus, Esmeralda and Quasimodo, aided by Madellaine, catch up with him. Sarousch almost escapes by threatening Zephyr, but Madellaine uses her high-wire skills to rescue Zephyr. Sarousch and his men are captured for their crimes.
At the festival, Hugo finally wins the heart of his longtime crush: Esmeralda’s pet goat Djali, after years of pestering him. A number of romantic couples proclaim their love for each other while Quasi rings the restored La Fidele, but the bell falls silent when Madellaine (who has now been dropped from all charges for her involvement of the theft) shows up in the bell tower. Having forgiven her, Quasimodo proclaims his deep and true romantic love for Madellaine and they share their first kiss while Zephyr rings La Fidele, ending the film.