Nan Harding is the new student at Mr. and Mrs. Bhaer's school. Everyone thinks that she is a pain in the head, but not Mrs. Jo. Together with the other kids, they all embark on their personal adventures and misfortunes while learning in school.

Charlotte is a girl who lives on a farm in Canada. On her 12th birthday, her father tells her that her mother, whom Charlotte has always believed to be dead, is actually alive and living in Paris, but soon she will arrive to live with them! Charlotte is very upset about this at first, but just when she adjusts to the idea, her father soon dies! Now Charlotte must face many challenges to live. She discovers that her father was from a noble family and her grandfather wants to force Charlotte to return to the family. She doesn't know her mother at all. Meanwhile, a landowner is trying to steal away her father's farm! Poor Charlotte...

The fairy tale follows a young man named Budori Gusuko in the Tohoku forests of northeastern Japan in the 1920s. After an onslaught of droughts and natural disasters, Budori is forced to leave his home and search for a better life elsewhere. Budori joins a group of scientists at the Ihatov Volcano Department, which deals with the same natural disasters that drove Budori from his home.

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.