Magic Knight Rayearth focuses on three eighth-grade girls: the tomboyish, headstrong but short Hikaru Shidou; the quick-tempered and no-nonsense only child Umi Ryuuzaki; and the intelligent and ladylike Fuu Hououji. While on a field trip to the Tokyo Tower with their respective schools, the girls find themselves drawn into another world, Cephiro. There they learn that Cephiro is influenced by one's will and that the Pillar maintains Cephiro through prayer. The girls are then tasked with rescuing the current Pillar, Princess Emeraude, from her abductor, the high priest and antagonist Zagato, after which they will be returned to Tokyo.
Guided by the creature Mokona on their quest, the girls discover their respective element-based magic and awaken the three Rune-Gods, creatures who can take the form of giant robots that the girls must pilot. As the girls progress on their journey, they overcome their differences, learning how to work together and accept each other as friends. After the girls find Zagato, they fight and are able to destroy him. After this, they finally reach where Emeraude is imprisoned, but the three learn that she had fallen in love with Zagato, which had hindered her ability to pray solely for Cephiro's well-being. Feeling responsible for her actions, she had imprisoned herself, and eventually summoned the Magic Knights to kill her, as no one from Cephiro could harm the Pillar. Her dark side then takes over, seeking to destroy the Magic Knights for killing her love. After a short defensive fight against Princess Emeraude, the Magic Knights have no choice but to kill her. They then find themselves transported back to Tokyo.
The second part of the series deals with the complications caused by Princess Emeraude's death. Set a year later, it opens with the three protagonists struggling with their guilt and despair over their role in her death. Meeting again at Tokyo Tower, they find themselves transported mysteriously to Cephiro again, and discover that only a single piece of Cephiro remains, which holds a castle where the survivors gather to take refuge. With the Pillar gone, Cephiro is, for the most part, defenseless, and the girls are saddened to learn that a new Pillar must be chosen by the Pillar system before the whole planet is destroyed. Not only that, three warring planets have begun their attempts to conquer the Pillar-less Cephiro: Autozam, a technologically advanced world which intends to use the Pillar system to remove the pollution in its air; Fahren, whose childish ruler Lady Aska plans to use it to turn Cephiro into a world of her whims; and Chizeta, an overpopulated world whose sibling rulers Tatra and Tarta plan to use it to make Cephiro into a colony.
As the Magic Knights help defend the castle, they each agree that the fate of the planet should not be the responsibility of only one person which, like Princess Emeraude, effectively prevents that person from ever being able to live and love freely. What's more, there is a mostly unspoken risk that when a new Pillar is chosen, something may eventually hinder them from praying solely for Cephiro's well-being, cause them to summon new Magic Knights to kill them, and bring Cephiro to near-destruction again until a new Pillar is chosen, causing the cycle of events to continue endlessly. As such, Lantis, a powerful magic swordsman and Zagato's younger brother, wishes to end the Pillar system for those reasons.
Eventually, Mokona narrows the candidates down to two: Hikaru and the sickly Eagle Vision of Autozam, who is friends with Lantis and, as such, wishes to end the Pillar system for him with his eternal sleep. As the two undergo the test to become the new Pillar in a recreation of Tokyo, Mokona reveals itself to be the creator of Cephiro and its laws, both of which it had created after sadly witnessing the violence and destructive nature of the people on its earlier creation, Earth. It was responsible for bringing the three girls back to Cephiro. In the end, Hikaru becomes the new Pillar of Cephiro, and brings Eagle Vision back to Cephiro from the Tokyo recreation with the help of Fuu and Umi, against Mokona's insistence that only one may return. Hikaru then rejects the Pillar system, decreeing once and for all the fate of the planet should not be the responsibility of one person. Mokona accepts their decision and leaves with the three Mashin. The manga concludes with the three girls returning to a new Cephiro to visit their loved ones, as they work with the rulers of the other planets to solve their planets' problems, and contemplate Mokona's wish to allow the three protagonists to bring change to Cephiro.
