Madeline: Lost in Paris is a 1999 direct-to-video film. It features Madeline being kidnapped by a man pretending to be her uncle so that he may claim her inheritance. Compared to the episodes and other movies of the franchise, this movie has rather dark themes.
It is wintertime in Paris and the girls all set off at half-past nine in two straight lines, as part of their usual routine. However, they soon learn that Miss Clavel has a cold, so they call Dr. Cohn to come and treat her. Meanwhile, Miss Clavel is interrupted by Pepito, who is practicing the violin next door. He promises Madeline that he will not play again until Miss Clavel is well again. Dr. Cohn says for the girls to give Miss Clavel love and warmth, and that soon she shall be well. That night, the girls reminisce on the happy times they have with their families at home, especially the times when they too have been sick. Madeline tells them of the times she spent with her parents, but sadly she no longer has them to turn to since they died many years earlier thus believing she has no family left and is now an orphan. Heartbroken, the girls wail at Madeline's story, but are soon comforted by Miss Clavel, who was awoken by the noise. She reminds the girls that they all love and look out for each other, and that they all are just as much a family as anybody else, bringing peace of mind to all of the girls. Everybody returns to bed with sweet dreams.
After Miss Clavel feels better, a letter is delivered to the house, saying Madeline's long-lost Uncle Horst from Vienna is coming for a visit. Ecstatic that she still has a family, Madeline eagerly awaits his arrival. Uncle Horst (Jason Alexander) arrives later in the week, and is reacquainted with his niece, whom he remembers fondly. Madeline is pleased to meet him, and Horst presents all twelve girls with lace collars as a gift. Uncle Horst then announces that he has been made Madeline's new legal guardian, and that she is to accompany him to his hometown of Vienna, where she can attend a fine finishing school. Although nobody wants her to leave home-schooling and caring love, Madeline reluctantly agrees to go.
That evening, Uncle Horst returns to dine with the girls, as well as Lord Cucuface and Pepito's family. At dinner, Horst tells of the Austrian School to the girls, certain that it will be more fulfilling than Madeline's current boarding home-school. The girls, wanting to prove that their home is just as good, puts on a musical to display their talents to Uncle Horst. Horst, however, does not sway from his intent and informs Madeline that they leave the next morning, while assuring her that she will come to love Vienna. Uncle Horst leaves for his hotel that night, during which Lord Cucuface reminds him of Madeline's inheritance, which Horst says he will be responsible for.
The night before Madeline is to leave with her uncle, Pepito tried and failed to stop the sun from waking up by preventing the rooster from doing his morning crowing. Soon, Madeline leaves with her uncle for Gare de l'Est where the Orient Express will take them to Vienna. Before leaving, Miss Clavel gives Madeline her mother's beaded necklace, which she was to give Madeline "at the right time". The two then depart for Vienna. However, the man thought to be Madeline's uncle instead took her on the Paris Métro and to an unfamiliar part of town, even abandoning her pet dog Genevieve on the way. Realizing that she is being kidnapped, Madeline throws pieces of her necklace to make a trail to where she is taken to. Madeline is soon kidnapped to an underground lace store run by a woman named Madame LaCroque, (Lauren Bacall) where Uncle Horst accidentally reveals that he is French, not Viennese German as he had claimed. It is then revealed that Horst isn't her uncle at all, but a man named Henri, a failed actor who could only do accents. He is Madame LaCroque's henchman. Madeline is led to a sweatshop in the basement, full of kidnapped orphan girls who are forced into making laces to sell. One of the girls, Fifi, befriends Madeline.
Shortly after Madeline left, Miss Clavel, the girls, and Pepito tried to stop her and Horst so that Pepito could give her his Halloween parting gift: A shrunken head from Brazil. They arrive at the train station, only to learn that the two had taken the Métro, not the Orient Express. They also find Genevieve abandoned at the station. Fearing the worst, Miss Clavel enlists the police to help them rescue Madeline.
Meanwhile, at the lace shop, Fifi's cough turns one of LaCroque's laces yellow. LaCroque, at the peak of her madness, bans her from using white lace, and is forced instead to make black lace in the dark, which could potentially render her blind as explained by one of the girls whose grandmother lost her sight that way; Madeline defends her in the process, but she ends up being thrown into the prison cell for talking back. Madeline sings a song of love along with the other orphans. Fifi tells Madeline of how LaCroque was once a cabaret dancer who had once torn her dress and fell off stage when performing. In total humiliation, she refused to perform again and sold her long hair to make lace. She then went into the lace business and kidnapped all of the Orphan girls to work as her miserable slaves. They tried to escape but they all got caught by LaCroque and Henri, and LaCroque cut their hair to make lace as punishment, including Fifi's to make into black lace.
Meanwhile, Pepito and Madeline's friends go off to find her on their own and discover the trail of beads that led to the lace store. A customer tells LaCroque she wants red lace, which gives her the idea to cut off some of Madeline's hair off.
Madeline tells her new friends when an escape plan fails that they may be small, but can follow as one. LaCroque interrupts and cuts off a few locks of Madeline's hair and prepares to torture her and the other orphans and deciding to give all of them haircuts. Miss Clavel and the police were able to discover the so-called uncle after a boy trips him after Henri refused to give him any change.
While Madeline is still in the lace factory, Pepito and the girls use the shrunken head to first knock off LaCroque's wig-(revealing her bald head), and then frighten her to the ground. Meanwhile, Miss Clavel and the police work out a plea bargain deal with Henri, in which that he will receive a lighter punishment if he helps the police and help Miss Clavel locate Madeline, to which he accepts.
Madeline and all of her friends are able to tangle La Croque in lace just as the police arrive with Henri and Miss Clavel. Henri, feeling guilty, tries to escape, only to be tripped by Pepito's spool trick, allowing the girls-(including Madeline) to tangle him up as well. The criminal duo are arrested by the police and taken to jail for several years as punishment for their crimes. However, the other factory girls still have no families or place to call home. LaCroque's lace factory has been permanently closed down and demolished.
That night while in their beds, Madeline's friends talk about what they would do with the reward money. Danielle would go shopping for fashion, clothes and jewelry, Chloe would travel to exotic countries around the world, and Nicole would own a zoo "with all of her favorite animals". However Madeline has a great plan in mind, though.
Sometime later, it is revealed that Madeline has used her reward to open a special school for the orphaned girls-(she also reunites with Fifi who now has long hair and is completely healthy and fully recovered thanks to Dr. Cohn who had given her treatment) and as a result, having realized that she has family all around her. All of the girls from both schools rejoice in the fact that they are all one whole family.