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.

Junior high school student Miaka lives a normal life in Tokyo until she finds a mysterious book in the library, and she and her friend Yui are transported the Universe of the Four Gods. Upon arriving in this new universe, the girls are immediately attacked by would-be slavers and saved by a dashing young man. When Miaka isn't looking, both Tamahome and Yui vanish. Unbeknownst to Miaka, Yui has been sucked back into the real world. Back in the library, all she can do is read on as Miaka sets out for the city to find the mysterious young boy and save her friend. But what awaits for Miaka isn't what either of the girls expect—and now Miaka's only way back to her world is to become the Priestess of Suzaku and save their world.

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.