Ayato Kamina was separated from the girl he loved, Haruka Mishima, when an event occurred that was thought to have killed everyone outside of Tokyo. But one day three years later, invaders suddenly attacked the city. It was then that he meets an agent of TERRA, Haruka Shitow, who tells him that she will give him the truth about the world. It is the beginning of a series of strange events, which involve him activating a giant mecha, the RahXephon and finding out that many people, including his own mother, has blue blood, and that he was actually living in a self-encased dimension where time moves slower than that of the outside world.

The story takes place in an alternate reality based in the year 1996, where humanity is advanced enough to develop long-range space travel, as well as bases on both the Moon and Mars. However, the Cold War tensions between the United States and the Soviet Union have not ended; rather, they've escalated as both sides build military facilities in space, and the shadow of nuclear conflict looms over humanity, both on and off Earth. Meanwhile, on the Red Planet, an exchange program created by the United Nations to promote peace and understanding is about to begin; the "Cosmic Culture Club," consisting of 16 boys and girls, as well as their instructor Elizabeth, arrives at the UN Mars base. Among the passengers is Anna a 14-year-old girl who serves as the narrator for the story. Suddenly, four unidentified humanoid robots classified as Super Powered Tracers are detected, engaged in fierce combat with each other. The UN base is caught in the crossfire and quickly destroyed, killing all but six members of the "Cosmic Culture Club"—Elizabeth, Arthur, Roan, David, Simone and Anna, and leaving them stranded on an inhospitable planet that has suddenly become a battlefield. As the battle ends, the lone SPT standing lands next to the terrified group and opens up revealing a pilot, who simply announces to them, "Earth is at stake."

This story takes place about one hundred years ago. Nadja is a bright, cheerful girl who was raised in an orphanage near London, England. Nadja was entrusted to the orphanage when she was a baby. So she thought her father and mother were dead. But before her thirteenth birthday, she found out that her mother might be alive.. Nadja sets out on a journey to find her mother! With all of Europe as the stage, Nadja's exciting adventure begins!

The kingdom of Gemini is attacked by the evil Queen Halle. The twin princesses of the kingdom are missing, so is the important Night Star Box, which has affected planets including Earth. The fairy Queen had sent Prince You Le and Sally to Earth, looking for the Night Star Box with the help of Maggie and Michelle. Then the gang found out one of the girls who takes dance lessons with Maggie and Michelle is one of the missing princesses, Bei Bei! The mission to find the Night Star Box and the the still missing princess, Ya Ya, is now on the shoulder of the fairies. (Source: Mahou Shoujo Wikia, edited)