Three girls named Anita, Michelle and Maggie are hired to protect Japanese author Nenene Sumiregawa during her stay in Hong Kong. In an incident where the "Paper Sisters" save Nenene from a disgruntled author, Nenene discovers that the sisters have the capability to control paper at their own will - an ability once used by her long-lost friend Yomiko "The Paper" Readman. Arriving in Japan after an airliner incident, the Paper Sisters move into Nenene's apartment and become her freeloading bodyguards.

Having recovered emotionally from the death of her brother Keough, Yufa, an acolyte, and her childhood friend, the swordsman Roan, set out for a new journey across the Rune-Midgard Kingdom. They are joined by the merchant Maya, the magician Takius, the hunter Judia and their old companion, the assassin Iruga. However it seems all is not well in this world, especially since Keough, who was believed to be dead, starts appearing to them once again...

The city of Tokyo has been overthrown, taken over by Invaders who have devastated the rest of the planet. For 15 years, the remnants of the human race have fought a losing battle against the Mu and their Dolem, knowing that the key to victory lies within the domed walls of Tokyo Jupiter, where time flows in a different path and none of the mind-wiped citizens even know that the city has been conquered. But no one has been able to get into Tokyo. Until now. Prepare for the ultimate paradigm shift as one young man learns the horrifying secret in RahXephon.