A Wrinkle in Time is the first in a series of four book that follow the adventures of Meg Murry and Calvin O'Keefe. The book begins by relating Meg's personal struggles at school and her inability to fit in with the crowd. This is also a problem for her younger brother Charles Wallace. Everyone thinks he is dumb, though both children are extraordinarily intelligent - indeed, Charles Wallace could easily be considered a genius. Beyond that, Charles Wallace also has the unique gift of being able to read the minds of others.
Charles Wallace befriends a strange group of women living nearby - Mrs. Whatsit, Mrs. Who, and Mrs. Which. These three ladies soon take the children on a strange journey, promising to help them find and rescue their father who has been missing for two years. One afternoon, after meeting Calvin near the ladies' house, the three are swept off to another planet, Uriel, through the process of the tesser - the process of wrinkling space and time.
On Uriel, the children are given a view of the Dark Thing, a massive blackness that threatens to overtake the universe and that is threatening Earth. It is only through the work of great figures such as Jesus and Buddha and Gandhi, as well as other great artists and scientists, that keeps the Dark Thing from overtaking earth. The ladies tell the children that this is what their father is fighting.
After a visit with the Happy Medium, an oracle who tells them what path they must follow, the children are taken to the planet of Camazotz, a planet overtaken by the Dark Thing. On Camazotz, everyone acts exactly like everyone else and all creativity has been expunged from the planet. The children meet the Man with the Red Eyes who tries to "hypnotize" them into following IT. Charles Wallace eventually gives in with the hope of defeating the Dark Force, but he is taken in by the powerful evil.
They are then taken to see Meg's father who has been imprisoned by IT. After Meg heroically rescues him from his glass chamber, Charles Wallace, still under IT's influence, takes them to see this IT. IT turns out to be a large, dismembered brain. It pulses and tries to hypnotize both Calvin and Meg, but Mr. Murry saves them both by tessering off the planet just as they are about the fall under its power.
On another planet, Ixchel, Meg is healed by a giant, tentacled beast called Aunt Beast. Aunt Beast shows her the meaning of true love and soon gives her the strength to offer her self to save Charles Wallace. Alone and back on Camazotz, Meg confronts IT face to face, and, using the only power that IT does not have - love - is finally able to defeat it. IT only wields the power of hate, and almost overtakes her, but Meg's love for her brother is stronger than the hate of IT. As she and the rescued Charles Wallace embrace, they are tessered back to earth where they are reunited with their family.