Aoi was raised as a normal boy on Earth. Little did he know he was the heir apparent to Mito, the Queen-turned-Space-Pirate of an alien race that chooses their sex at puberty! Aoi fell in love with Mutsuki, the police officer who was chasing Mito, and the three of them saved the Universe. The only side effect was that Aoi blossomed into a beautiful young woman.

Now a malevolent entity calling herself the true Queen of the Universe appears with enough power to destroy entire planets. Aoi must defend her new throne, but she needs Mutsuki's help. Mutsuki must come to terms with her own feelings for Aoi so they can defend Earth together and become the galaxy's first royal pair of queens.

Due to the recent events that happened on the last episodes of the season, the Goddess have some stability problems with their body systems. The always adult looking Urd becomes a little girl and has a fateful encounter with a boy, whereas little Skuld becomes an adult and wants to experiment adulthood together with Keiichi.

Miaka and Taka (Tamahome's reborn out-of-the-book self) return to the Universe of the Four Gods to try and restore Tamahome's memories to Taka. This is not as easy as it sounds, however, when the evil Tenkou shows up to rain on their parade. He manages to thwart most of their attempts at getting Taka's memories back, and uses his newfound power to summon the Gods outside the book. (Source: ANN)

A year after the events of Fushigi Yuugi, Tamahome is pulled back into the book and is sent on a complicated ride through illusion, confusion, and betrayal. Meanwhile, Yui is acting oddly and Miaka is heartbroken over the loss of Tamahome, while Keisuke and Tetsuya try to discover what is going on with the book. (Source: ANN)