The story begins when high school student Kazuki Muto is killed one night saving a mysterious girl from a monster, only to wake up in his school dorm, believing it to have been a dream; however, he soon finds out that dream wasn't a dream at all when a giant serpentine monster attacks him and his sister. Tokiko Tsumura, the girl he saved, explains that the monster is a homunculus. Kazuki had been attacked and killed by it when he was rescuing her; however, she, feeling responsible for him, revived him by placing a Kakugane medallion in his chest, serving as a replacement heart.
Yuru, a young hunter, lives in a small village deep in the mountains, hunting wild game and leading a humble life with Asa, his younger twin sister. Their peaceful lives are torn apart when a dragon’s roar echoes across the sky. What secrets lurk within their village? What fate awaits them?
Ten years ago, a child wished for the destruction of the world. Now, a group of people has the ability to grant their wishes depending on their power. They are called "Order User." Before these great people who have the power of "Order," one person excels the most with the ability to rule and conquer the world and turn people into puppets when it is in his jurisdiction. This power belongs to Hoshimiya Eiji, who is also responsible for the destructive phenomena that happened exactly ten years ago.
In a distant future, Tetsuro is a human boy who wants his body replaced with a robotic one. This is possible, but to do so he has to reach the Immortal Planet onboard the space train Galaxy Express 999. Maetel, a beautiful and mysterious blonde woman dressed in Russian style, joins him in the long journey through space. Every episode sees our heroes arriving in a new planet's space train station.