Mary Smith relocates to the serene countryside of northern England to stay with her Great-Aunt Charlotte. Initially feeling bored and friendless, the young girl attempts to help around the estate with various chores, but her efforts often lead to comical mishaps. She becomes the target of teasing from a local boy named Peter, who pokes fun at her clumsiness and her wild red hair. However, Mary's encounter with Peter’s cats, Tib and Gib, leads her to discover enchanting glowing flowers that pique her curiosity. A local gardener informs her that these flowers, known as "fly-by-night," are believed to possess magical properties coveted by witches.
The following day takes a dramatic turn when Gib mysteriously vanishes. Tib guides Mary to a broomstick, but in her excitement, she accidentally breaks a bulb from a fly-by-night flower on it. This mishap releases a surge of magical energy that brings the broomstick to life, allowing Mary to experience the exhilarating sensation of flying like a witch. This adventure lands her at Endor College for witches, a magnificent complex of buildings soaring above the clouds.
Upon her arrival, Madam Mumblechook, the headmistress, mistakenly believes Mary to be a new student accompanied by her familiar, Tib. She gives Mary an insightful tour of the prestigious college, where she encounters Doctor Dee, the esteemed chemistry instructor. Mary soon discovers that she possesses a remarkable ability to perform advanced spells, such as invisibility, surprising everyone with her talents and distinguishing red hair—a significant trait among formidable witches.
However, when Mary confesses that her magical prowess stems from the fly-by-night flowers, and that Tib is Peter's pet, Madam’s demeanor shifts dramatically. She reveals her true sinister nature and allows Mary to leave only after extracting Peter's whereabouts. That very night, an ominous message arrives from Madam, revealing that she has kidnapped Peter. The demand is clear: Mary must bring the fly-by-night bulbs to Endor. In an act of bravery, Mary and Tib race back with the bulbs, only to find themselves captured in Madam and Doctor Dee's transformation laboratory.
While imprisoned, Mary discovers that Peter is also trapped and learns of Doctor Dee's cruel experiments on animals, including Gib, transforming them into bizarre creatures. Utilizing a spell she took from Madam's office, Mary manages to reverse the transformations and unlock their cell. They make a daring attempt to escape on the Little Broomstick, but Peter is recaptured in the chaos, and Madam vows to extract her revenge for the stolen flower and the spellbook.
In her flight, the Little Broomstick transports Mary to a secluded cottage on a tiny, animated island. Inside, she unearths spell notes and a magical mirror used by Great-Aunt Charlotte to communicate with her. Through mystical visions, Charlotte reveals that this cottage was once her home and that she, too, was a talented red-haired student at Endor. Charlotte recounts how she found the fly-by-night flower, triggering a dangerous obsession in Madam and Doctor Dee to transform humans into witches. When their experiments ultimately failed, Charlotte fled, taking the flower to keep it safe. She urges Mary to use her remaining bulbs to return home, but Mary firmly resolves to save Peter.
Determined to rescue her friend, Mary returns to Endor, where she finds Madam and Doctor Dee attempting to turn Peter into a warlock. Their experiment ends poorly, resulting in Peter being trapped in a monstrous gelatinous form. In a frantic bid to aid him, Mary delivers the spellbook, which allows Peter to revert the transformation and dismantle all of Madam and Doctor Dee's nefarious research. Flying home together, Mary discards her last fly-by-night bulb, declaring that she no longer needs any magic in her life.
