Hazuki Azuma has developed a sexual attraction to her adopted older sister Hatsumi. Hatsumi, however, disappears on the morning of her 16th birthday. Hazuki goes world-hopping in search of Hatsumi along with her companions, a Kansai dialect-speaking bird, Ken, and the hat-wearing Lilith known as Eve.
On board the train, Yoko smacks down the Colonel and is sheltered by the Siberian Tiger who brings Adam to her. They are then confronted at gun point by the drunk and train conductor who are also undercover spies. Everyone except her is killed, however the Siberian Tiger is a double agent and sends her through the window. Yoko recovers and with Hazuki take down Siberian Tiger. Hazuki, who had helped Adam earlier, helps Yoko to find the bomb and hands over the decoder at the destination.
Hazuki arrives in the Great Library and meets Lilith, who develops a crush on her because she contains the essence of Yami, once the protector of the Great Library and Lilith's lover. Hatsumi turns out to be an incarnation of Eve, who Lilith wants returned to the Library. Hazuki unenthusiastically accepts Lilith's help traveling the worlds.
Milka is saved by her white tiger. Arya reveals that Seiren was a demoness spawned by Lilith; Seiren was only interested in harnessing Milka's power. Hazuki and Lilith give their boat to Milka and return to the Great Library, fixing the torn book and curing Milka. A long flashback shows Hazuki and Hatsumi's life before the latter's disappearance.
Hazuki saves a cute fox spirit, Meirin, from a band of samurai in a feudal Japanese world. She encounters Princess Fuji, who looks identical to Hatsumi except that she speaks. She also uses the same ornate comb that Hatsumi had, and the legend about the comb is the same Eve legend. Ninjas intent on gaining Princess Fuji's mysterious power attack the mansion while Lilith and Meirin ride their coattails in. Inspired by Kaguya-hime.
Lilith foils the ninjas’ attempts to steal the comb by accident, while a charged up Hazuki rescues Princess Fuji from the head ninja. Lilith casually says that the presence of the comb means that Eve was in this world. Meirin gets summoned to Gargantua's dimension because he thought she had the comb. Princess Fuji had actually given it to Hazuki, and they embrace in the moonlight. A long flashback then deals with the aftermath of episode four, when Lilith accepted Mariel’s soul from Gargantua in exchange for a world of his own. He still refuses her charms and resolves to find Eve, the source of eternal life.
Lilith appears in Gargantua's world but dimension-doors out. A nine-tailed fox spirit opens her own door into Gargantua's world; Gargantua and his troll trio charge through and find themselves in a world of rooms which link to many worlds. Meanwhile Lilith and Hazuki arrive aboard a colonization spaceship where a computer is caring for a whole cohort of children whose parents have all become "immobile" and which is itself failing and malfunctioning. A habitable planet must be found soon for the survival of the children.
With Lilith’s help, the ship warps within reach of a suitable planet. Hazuki learns that an Eve incarnation called Lular appeared and then vanished on board a hundred years ago. The children land on the planet with the DNA samples of Earth's animals; later, Lilith and Hazuki arrive in the universe garden. They meet Gargantua and his trolls, Mariel, Tamamonomae. The latter easily removes Lilith’s Hat, reducing her to tears.
Gargantua, Hazuki and Lilith all argue over Jill/Hatsumi/Eve, who stops their bickering. She consents to Tamamonomae returning the Hat to her head and disappears back to the Great Library as a result. It seems that in most of the worlds where she has been her disappearance has not left any major problems — except for the three who have been pursuing her across worlds. She then tries to set things right. Gargantua finally realizes that it is Ritsuko that he loves rather than Jill. He rescues her from her cell and reshapes his world into a bright and cheerful one where he and Ritsuko, who seem to have been made immortal by the Door of Eve, can live together happily ever after.
Lilith lashes out at Eve for abandoning her in the Great Library for what seems to be tens of thousands of years and Eve tries to make it up to her. Lilith notices that Eve misses Hazuki, who seems not to have returned to the correct book-world. Alone again, Hazuki reflects on her dreamlike adventures, but suddenly sees Hatsumi returning to the house. History repeats itself, like a universe reset, but Hatsumi does not glow and disappear at the stroke of midnight. Instead Hatsumi and Hazuki share a passionate kiss and then a cuddle. Hazuki awakens the next day not remembering anything, but notices the signs of Hatsumi's future rebirth as her child.