Meg Murry is a thirteen-year-old, plain-looking girl who can't seem to get along at school, despite unusual intelligence and a wonderful family. Impatient by nature, she quickly gets into trouble with her teachers, though the real source of her unhappiness is her missing father, who vanished a year ago on mysterious government business. Meg has two younger, perfectly normal twin brothers, Sandy and Dennys (10-years-old) and an extraordinary 5-year-old brother, Charles Wallace, who has intelligence and intuition beyond his years. Their mother, Mrs. Murry, is a Ph.D. like her husband, Mr. Murry, and while she tries to focus on her work and on the children, she is very unhappy and worried by her husband's absence.
One stormy night, an old funnily-dressed woman shows up at the Murry's house: Mrs. Whatsit. Though Charles seems to know her, Mrs. Whatsit has come to deliver a message to Mrs. Murry: there is such a thing as a tesseract. Meg and Charles are mystified by the incident, and go to find Mrs. Whatsit the next day for answers (she's staying at a supposedly haunted house just off their property). On their way there, they come across Calvin O'Keefe, an athletic and popular boy who Meg knows only vaguely from school. It turns out that like Charles and Meg, he is unusually intelligent, and possesses a gift for communication. Though at first suspicious of him, Charles thinks he must be a good egg, and allows Calvin to come along with him and Meg. Mrs. Whatsit is not there, but they meet her friend, Mrs. Who, and then the three children head home to the Murrys to have dinner. Calvin straightaway feels at home with the Murrys.
After Calvin has put Charles down for bed, he takes Meg for a walk in the garden behind the Murrys' house, and suddenly Charles, Mrs. Whatsit, Mrs. Who, and Mrs. Which (their third companion) are there. The Mrs. W's tesser the children to another planet (tessering is a painful but quick way to travel through space and time; a "wrinkle" in time), where they show them the Black Thing: a shadow that has fallen across many parts of the universe, representing Evil. The Black Thing has captured Mr. Murry, and the children must save him. They then tesser to another planet, where they meet the Happy Medium, an oracle-like woman who shows them in her crystal ball a way in which the Darkness can be destroyed: a star can gives its life to destroy the Black Thing, and that is precisely what Mrs. Whatsit did.
The time for action has come: Meg, Calvin, and Charles tesser to the planet Camazotz, an evil planet entirely taken over by the Black Thing, where Mr. Murry is. On Camazotz, everyone is exactly alike, every house, child, and adult is almost exactly the same. This is because every individual is controlled by IT, an enormous brain which thinks for everyone on the planet, destroying individuality. The children (whom the Mrs. W's can no longer accompany) find Mr. Murry and rescue him from his prison, but in the process Charles has his mind taken over by IT, and becomes ITs minion. This evil Charles takes his father, sister, and Calvin to IT, and Mr. Murry is forced to tesser himself, Meg, and Calvin away to save their own minds.
The three of them land on another planet in Camazotz's system, and Meg is instantly enraged with her father for leaving Charles. She has, however, been physically and mentally wounded by tessering through the Black Thing, and the tentacled natives of that planet (especially Aunt Beast) tend to her until she is well. A council is held with the tentacled natives, the Mrs. W's, and Calvin, Meg and Mr. Murry, and Meg sees that only she can save Charles from IT, since she knows and loves Charles best of all of them. She tessers with Mrs. Which back to Camazotz, and manages to free Charles from ITs grasp by simply looking at him and loving him, for love is the one thing IT cannot stand. They then tesser back to the Murrys' backyard, where they find Calvin and Mr. Murry also returned. Mrs. Murry and the twins, upon hearing the commotion, run outside, and a very happy family reunion ensues.