Mary is an ordinary young girl stuck in the country with her Great-Aunt Charlotte and seemingly no adventures or friends in sight. She follows a mysterious cat into the nearby forest, where she discovers an old broomstick and the strange Fly-by-Night flower, a rare plant that blossoms only once every seven years and only in that forest.

Together the flower and the broomstick whisk Mary above the clouds, and far away to Endor College - a school of magic run by headmistress Madam Mumblechook and the brilliant Doctor Dee. But there are terrible things happening at the school, and when Mary tells a lie, she must risk her life to try to set things right.