Madeline Dare has traded in the drudgery of living in backwoods Syracuse, New York, to work as a teacher at Santangelo Academy, a boarding school for emotionally disturbed teenagers in the Berkshires. Behind the ornate gates of the academy, she finds a disturbing realm where students and teachers must follow the dean’s bizarre therapies. From her first day, Madeline doubts Dr. Santangelo’s credibility, and she’s not afraid to voice her concerns.

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The Spanish Ambassador and his family have moved to London. Miss Clavel and the girls are invited to London for Pepito's birthday party and they buy a retired horse from the Royal Stables as a gift. Madeline and Pepito are riding the horse in the courtyard when it jumps the fence and joins the Queen's procession! That night, after touring the city in search of the children. Miss Clavel tucks everyone into bed. But the poor horse hadn't eaten all day...

Madeline falls into the Seine and is rescued by a courageous dog. The girls take home the collarless mutt and name her Genevieve. Lord Cucuface, the President of the Board of Trustees, insists that dogs are not allowed in the convent and his chauffeur takes Genevieve away. Miss Clavel and the girls search the streets of Paris for her but return to the convent disappointed and disheartened. Miss Clavel investigates a noise in the night - it's Genevieve!...

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.

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...

Madeline, Pepito and the girls visit Miss Clavel's aunt and nephew in their Alpine chalet. The trip is laden with adventure - from skiing and skating to an abominable snowman sighting. Later, when the group is trapped in the chalet by a terrifying avalanche, it is Madeline's spirit and ingenuity that saves the day.

The girls are looking forward to a big costume bash at Pepito's house. But a week or so before the festivities they all come down with chicken pox and are quarantined in the Old House. Then, when Dr. Cohn declares that they have recovered just in time for the party, Madeline helps everyone create costumes that incorporate their remaining "spots".

The circus has been cancelled because Monsieur Funnybones, the world's shortest clown, has lost his ability to laugh. When the forlorn performer shows up at the Old House disguised as a chimney sweep, Madeline teaches him that being tall is just a state of mind.

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.