Due to her father's remarriage, robust 16-year-old Himeno Awayuki moves into a large mansion with a beautiful garden—the quintessential dream house for any girl her age. However, much to Himeno's disappointment, her new stepfamily doesn't really seem to like her, as her stepmother often occupies herself with her father, her younger stepsister Mawata ignores her, and her other stepsister—the equally aged Mayune—tries to prank her at every opportunity. But Himeno doesn't have time to dwell into thoughts of hopelessness—her new life has now become involved with a group of seven magical boys known as the Leafe Knights, after they ask her to become a magical princess who can borrow their powers! Although Himeno accepts their request and becomes the Prétear, she feels doubtful in her abilities to protect the world and its Leafe, the source of energy for all life. Will Himeno be able to find happiness among her new family and also save the Earth from the enemy, the Princess of Disaster?

The story is set in the future on the planet named Amoi which is controlled by a supercomputer named Jupiter. Among the mostly male human population, the light-haired elite class is allowed to temporarily keep the dark-haired "mongrels" as pets. One elite member, Iason, encounters a mongrel named Riki in the slums and decides to take him in. However, Iason keeps Riki longer than it is socially approved, and rumors abound about their possible relationship.

Ever since the quiet and timid Reina Aharen enrolled in high school, she has made new friends and even started dating her classmate Raidou. When the two begin their second year, everything seems to be going well, as they are seatmates once more. Soon after, a transfer student named Riku Tamanaha joins their class. Unbeknownst to Reina, the outgoing and stylish girl is actually a childhood friend she separated from years ago. With Raidou's support, Reina is able to rekindle their friendship. Although they have grown closer, Raidou and Reina still struggle to communicate due to his overactive imagination and her difficulty with expressing herself. Nevertheless, the eccentric couple continues to brighten up the lives of people around them as they enjoy each other's company to the fullest.

In the year 2062, the world's two superpowers are fighting a long and brutal war. In a desperate attempt to win, pilot Kei Katsuragi is given the mission to detonate a super weapon called the Space/Time Oscillation Bomb. The bomb explodes but the results are completely unexpected: a multitude of dimensions, times, and realities are unleashed into the world. Can Kei reverse the effects and bring life back to normal?