The story begins when the Spanish Ambassador and his wife move in next door and their son, Pepito, is not a good boy. Madeline dubs him a 'bad hat' and the book is controversial due to the cruel nature of Pepito's mischief, notably animal cruelty and pulling various pranks.[1] After he suffers from his own actions involving a group of dogs and a cat, Pepito reforms himself while bandaged up in bed and Madeline visits him. Pepito is also a main character in the stories Madeline and the Gypsies and Madeline in London, but in the TV series, he has three cousins named Paquito, Pablito and Panchito who are much worse than he himself was.
Pepito, the son of the Spanish Amassador invites Madeline and her fellow students to a Gypsy carnival. However, in the chaos caused by a sudden rainstorm, Miss Clavel and the other girls lose sight of Madeline and Pepito, who are unintentionally left behind on the ferris wheel. The two children find themselves guests of the gypsies, and soon wind up part of the carnival themselves.
Madeline does her trick of frightening Miss Clavel and falls into the Seine River and is saved by a dog. Miss Clavel and the girls cannot find the owner of the dog, so the girls are allowed to keep the dog. When they bring her home, they name her Genevieve. But problem starts to rise when other girls want to spend time with Genevieve. Big trouble arrives in front of their animal-loathing Landlord Cucuface, who takes one look at poor Genevieve and has his driver take her away, causing the girls and Miss Clavel to look for Genevieve, only to be broken-hearted of not finding her. Late that night, Miss Clavel wakes up and finds Genevieve in the light of the doorway. Everyone rejoices Genevieve's return. That night, the girls fight about Genevieve again, causing Miss Clavel to take Genevieve to her own room. Even later that night, Madeline and the girls, with Miss Clavel find that Genevieve has given birth to eleven puppies, giving enough hound to go around.
At the Old House - and all over the neighborhood - people's hats, gloves and scarves are missing. Madeline and Pepito work with Detective Moreau to find the perpetrators, then finally discover that the "thieves" are some altruistic magpies who are distributing the warm clothes to the homeless in the park.
The Old House, sorely in need of repair, is condemned and the girls are forced to move to a small apartment where their snooty neighbors hate kids and dogs. But just before the wrecking ball destroys their beloved abode, Madeline enlists the aid of the ladies of the Historical Society, who help get the Old House renovated to perfection.
When Madeline and the girls visit a toy factory, Madeline is accidentally boxed as a "doll" and sold to a handicapped girl. The ailing child considers Madeline her only friend and is devastated when Madeline reveals her true identity and has to go home. But things turn around the next day when the little girl discovers she now has twelve real live friends.
Madeline, the girls, and Pepito prepare a disastrous meal for Lord Cucuface, who immediately enrolls them for cooking lessons at the famed Cordon Bleu. After various mishaps, the children finally get the hang of French cuisine, but Madeline fails to receive her diploma because she has given her creation to the hungry. In the end, Miss Clavel helps Madeline realize that the satisfaction of helping someone is more rewarding than any blue ribbon could ever be.
The girls get a chance to perform with a famed ballet master who thinks Madeline is too small to succeed. Madeline's insecurity (and Pepito's teasing) keeps getting in the way of her performance until she is given a pep talk - and a pair of toe shoes - by an accomplished prima ballerina, who convinces Madeline that hard work and courage will help her excel.
After being evicted from the opera for barking along with her favorite arias, Genevieve is dog napped by an impresario who sets her up at a dinner theatre. When Madeline finally catches up with her talented canine, Genevieve, now a star is reluctant to go home because she is still embarrassed about the incident at the opera. It is up to Madeline to convince Genevieve how much she is missed at the Old House.
Madeline paints a magnificent picture and accidentally leaves it at the Louvre, where it is mistaken for a masterpiece and hung next to the Mona Lisa, upstaging DaVinci's creation. Madeline tries to get the painting back, but one believes that she is the anonymous artist. In the end she finds she must use her feisty individuality to prove herself to the authorities.
Genevieve digs up a huge bone in the garden that turns out to be a fossilized stegosaurus' hip bone. The girls are thrilled with the discovery until the Old House becomes a dig site and is invaded by hordes of paleontologists and equipment. Calm is briefly restored after Miss Clavel convinces Lord Cucuface to donate the bone to a museum. But when Genevieve misses her beloved bone and runs away, it is up to Madeline to find her and to lure her back with something better.
To raise money to buy Miss Clavel a birthday present, Madeline starts a detective school. Meanwhile, Miss Clavel is receiving mysterious gifts of great value - jewels, a painting, etc. Inspector Moreau discovers they are stolen by the infamous cat burglar Le Chat and arrives to question Miss Clavel. Madeline and her students use their detective skills to apprehend Le Chat, who was once a reform student of Miss Clavel's and has been working at the Old House as a painter and gardener. The stolen items are returned, Le Chat is locked up and the girls discover that they do not need a lot of money to get Miss Clavel a present that she will always cherish.
After Miss Clavel inspires the girls to read more books, they decide to put on a presentation of "The Hunchback of Notre Dame." Pepito refuses to play the title role because he is embarrassed to portray an ugly, deformed character. In an attempt to change his mind, the group visits Notre Dame where a scary real-live hunchback swings down from the bell tower and carries off Miss Clavel! The "hunchback" turns out to be the dashing Gerard Dippity-doo, who is starring in a film version of the novel. Dippity-doo comes to the girls' performance, inspiring Pepito to show compassion for people with disabilities - and to play the role of the hunchback magnificently.
Lord Cucuface arrives at the Old House with a large chunk of prize-winning cheese (for fondue) and a new touring car. While Cucuface takes Miss Clavel for a calamitous driving lesson, the mice eat the cheese. The girls distract Lord Cucuface by putting him to sleep with a boring play, as Madeline and Pepito convince the reluctant Miss Clavel to take the car to replace the cheese before Lord Cucuface wakes up. The local cheese shop is out, so they end up searching for the cheese maker in the countryside where they get a flat tire, overheat, and run out of gas. In the end, they get towed back to town by the cheese maker’s horse - just in time to prepare some delicious fondue before Lord Cucuface wake up.
Madeline and girls visit Miss Clavel's cousin Fifi at the radio station for the Halloween broadcast and accidentally leave the microphone on as they tell a scary story about ants invading New York, which is broadcast "War of the Worlds" style all over the city, sending all of the metropolitan area into a panic.
The girls enter a cancan competition, but the intense practice schedule and concerns about costumes creates a problem: cliques. The girls break into groups and exclude and taunt each other until Madeline, with the help of two legendary cancan stars, has the job of helping the girls make amends in time for their final competition.
When Madeline's sinuses act up, Dr. Cohn suggests she go someplace warm, so Lord Cucuface sends the girls to Cannes. Not heeding Miss Clavel's warning, Madeline stays on the beach all day, and gets sunburned, so she's forced to stay inside. She is so lonely and bored, Lord Cucuface asks his director friends to bring their latest movies - and, on Madeline's suggestion, a contest - The Cannes Film Festival is born.
Madeline and the girls play matchmaker and are invited to be in the resulting wedding. However, Madeline's feelings are hurt when Pepito starts ignoring her, not knowing that he's being ruthlessly teased by his cousin Pablito for "liking a girl". When she learns the truth, she convinces them it's okay for them to be just friends.
Nicole is embarrassed when she is asked to read a letter from her aunt, and it is revealed that her reading skills aren't as developed as the other girls. It turns out that her aunt has sent tickets to her and the girls to go to Africa. With Lord Cucuface tagging along, Miss Clavel and the girls join Nicole's aunt for a safari. There, they meet a friendly little gorilla named Rosie, and thru her, Nicole learns that she shouldn't be ashamed of being a late bloomer.
When the pipes burst and the old house is closed for a plumbing overhaul, Madeline and the girls move into Lord Cucuface's lavish suite at the Ritz. While there, they help a lonely rich girl and a hungry homeless girl, and soon discover that they'd rather have each other's love than live an empty upscale existence.
When Miss Clavel brings in a "method" acting teacher to direct the girls in a play, Madeline is sure she will get the leading role. Disappointed when given supporting roles (as trees) Madeline and her friends plan to boycott the play, until Madeline discovers that even small part can be important and fun, and that the girl who won the lead really deserved the part.
After Pepito burps at the dinner table, his parents insist on sending him to etiquette school, where he is joined by Madeline and the girls. After they graduate, Pepito's unruly cousin Pablito tries to convince Pepito that manners are uncool, but Madeline helps Pepito see the light just in time for him to put on his best behavior during an event for the soccer star Pepe Pelota.
The girls are planning a spring tea in honor of Lord Cucuface and the trustees when Sugar Dimples, the child movie star, drops in to visit and takes over, turning their simple party into a major "Hollywood" production, with over-the-top results. It is up to Madeline to bring the party down to earth and remind Sugar Dimples that it is the company that counts, not the lavishness.
When Lord Cucuface becomes suddenly indisposed, Madeline takes over his mission to impress some American tourists who are potential donors to the girls' school. She tells them that she is a famous tour guide, and finds she must lie more and more as she takes the eccentric couple around the Louvre, until they are all hopelessly lost and she is forced to come clean and tell the truth.