With Nenene safe and no longer suffering writer's block, Linho terminates the Sisters' employment, so they must prepare to go back to Hong Kong. A depressed Anita finds it difficult to say goodbye to her classmates, especially Hisami. When Hisami avoids Anita's farewell party, Tohru convinces Hisami to return, and Anita and Hisa make their proper farewells to each other at last. Because Anita is leaving, Junior decides to retrieve Richard's book. Nenene gives the Sisters a standing invitation to visit her in Tokyo any time, and will accompany them to Hong Kong before they say goodbye. When they arrive at their Hong Kong apartment, a horde of Dokusensha soldiers ambush them, along with Lee Linho--preparing to capture Nenene.

When Nenene wanders off without her bodyguards, the Sisters follow her to Jinbo-cho. Michelle quickly forgets her mission and enters a shopping frenzy, while Maggie passes out from the excitement of being surrounded by all the bookstores. Anita manages to find Nenene, following her to the underground store, Toto Books, where she meet a strange young boy (Junior). Nenene and Anita drop books off at Yomiko's apartment and discuss Anita's aversion to books; meanwhile Michelle has bought so many books that the Jinbo-Cho store owners start a rumor that Yomiko Readman has returned.

Anita returns to her school, where everyone's behavior just seems slightly off: Hisa likes Tohru, Chiho is shy, and Natsumi is embarrased by her sisters' accomplishments. Wendy Earhart approaches Anita, offering Anita a chance to have her memory re-written just like her classmates, in exchange for freedom and a few tissue samples. Anita decides she cannot live a lie and returns to Nenene's apartment, where she runs into a tearful Yomiko. Despite Anita's resentment, she agrees to team up with Yomiko to sabotage the Jinbo-Cho satellite dish and capture Joker. They take him hostage and fly back to Saitama to rescue Michelle, Drake, and Nancy, who are being surrounded by British Library troops.

Nenene's editor Lee Linho hires the Paper Sisters to remain in Japan to look after Nenene. However, after fighting over money woes, they decide to pay Nenene a visit, quickly imposing on her hospitality--and breaking her television. They use Lee's deposit money on their new apartment to replace Nenene's television, but this leaves them homeless, so Michelle concocts an overly complicated scheme to guilt Nenene into taking them in. While the plan initially fails, Nenene eventually repents and allows them to live with her. Meanwhile, on the news, Joker is seen with United States President Cole.

Nenene Sumiregawa, a famous Japanese author travels to Hong Kong for a book signing. She meets Michelle and Maggie, two of the Paper Sisters, who have been hired to be her local guides. When Nenene's hotel suite is bombed, the Sisters volunteer to help protect her. After spending the night at the Paper Sisters' apartment (where she meets the third sister, Anita), a jealous rival holds her hostage at her book signing, but he is foiled by the three sisters. Nenene is excited to see their Paper Mastery, but is disappointed to learn they have no connection to her friend, Yomiko Readman, who has been missing for four years. When Nenene is attacked on her way home to Japan by another rival, the Sisters follow and rescue her.

Anita runs off into the woods and has to be calmed by her sisters; meanwhile Yomiko makes further explanations to Nancy, Junior, Drake, and Nenene. A British Library agent called Mirror Man infiltrates, forcing Junior to return to duty. The next morning, everyone except Anita and Yomiko has gone missing. Taking the appearance of Nenene, the Mirror Man tricks them and steals the book, but they escape his trap are ready to fight.

Nenene insists Anita go to school, and so Anita enters the local seventh grade class. She meets and befriends the girls in her class, including the shy Hisami Hishishii. Anita ends up joining the library club to hang out with Hisa. During their chat, an English man named Richard shows up, trying to hide a book; however, he gets shot from an unseen assailant and passes the book to Anita. Anita is attacked by the shooter, who has the power of intangibility. But Michelle--who had shown up at the school to see how Anita was doing on her first day--appears and helps drive away the assassin. One of Anita's classmates, Tohru Okahara witnesses part of the fight, but chooses not to confront Anita about it (despite his rivalry with her). In the meantime, Nenene sneaks away to follow a lead on the missing Yomiko, and the Sisters receive a job order from Dokusensha.

The Paper Sisters travel to Romania to retrieve a book stolen during the fire at the British Library four years ago. While attempting to infiltrate Professor Webber's castle, their powers are partially stripped by a strange force surrounding the castle, and they are attacked by strange animals. Maggie grows excessively depressed while Anita grows extremely frustrated and begins to pick fights with her sisters, then runs off. The three finally find Professor Webber's central chambers, where they discover he has been weakening their abilities and playing on their emotional weaknesses with the influence of ultrasonic and subsonic waves. Michelle finds herself partially immune because of her general sense of calm, and the Sisters find a way to defeat the sonic attacks. Anita kills Webber and they flee. An already injured Maggie protects Anita from Webber's vengeful servant Irving, and Dokusensha agents Kim and Sonny Wong help the sisters escape the castle.

Anita's school day routine is shaken when her teacher announces the annual "Family Visit" day, and she tries to keep the knowledge of the day from her sisters, planning to skip class herself. She runs into Junior , who has been disguising himself as a student, searching for the book Anita hid in the library. When the household learns Anita has kept the family visit day--and accompanying required book report--a secret, Maggie and Michelle discuss Anita's aversion to books and reveals they are adopted, not blood related. Although Anita doesn't expect her family to appear for the visitation day, she decides to do a book report anyway, reading her first book in a long time--Nenene's "Midnight Liberation Zone."

The Paper Sisters arrive in a small town searching for a retired actor named John Smith, who possesses one of the British Library books. However, after Michelle's disappearance in a cafe, Maggie is arrested, accused of killing her. Anita is left alone and then nearly attacked by someone posing as Michelle. While Maggie breaks out of jail, Michelle frees herself from a coffin and finds herself in a writer's apartment, where she learns about Smith. She figures out who Smith is and forces him to release her sisters and give up the book.

Every night, the school library has been trashed, and Anita's classmates blame the intrusion on a poltergeist. They decide to stay in the library overnight to investigate. Anita invites Junior to the ghost hunt, and interestingly enough, the "ghost" fails to make an appearance. The students have fun partying in the library regardless, and Tohru finds a moment alone to try and confess his feelings to Hisami. Meanwhile, Anita finds Junior alone and keeps him company while they watch the stars. Anita reveals the location of the hidden book to Junior--but after having his moment of friendship with Anita and meeting Michelle, Junior reports to Wendy that he was unable to find the book.

Dokusensha sents the Paper Sisters to a hot springs resort in order to retrieve another British Library artifact, known as "the Key," from archaeologist and special agent Alice Alice Arquette. Coincidentally, Nenene is at the same location for a school reunion/wedding reception. Arquette, has hired Drake Anderson as her bodyguard, and they and the sisters have a face-off in the resort cafe, where Nenene discovers them. The writer follows the Sisters while they chase Alice and Drake into a cave. The Sisters find themselves at a standoff with Drake while Alice retrieves the Key--when suddenly Sonny Wong arrives and brutally slaughters Alice. Even though the Sisters are supposed to be on the same side as Wong, they protect Drake, disgusted by Wong's brutality. Junior appears, masked, and steals the Key. Drake floods the cave and helps the Sisters and Nenene escape. The Sisters receive only partial payment for their "assistance" to Mr. Wong, which they refuse.

Nenene receives two Christmas party invitations, the first of which she discards as being sent by a lunatic. The sisters talk her into accepting the second invitation, to the 10th annual Young Writer's Award reception (Nenene had been the inaugural recipient of the reward). After dodging loopy authors and snotty editors, Nenene announces she has begun work on her new novel. When they return home, the Paper Sisters reveal they sent the first invitation: a "birthday" party for the three of them. They tell Nenene about their first meeting, two years ago to the day, in an abandoned church in Hong Kong. The young Dokusensha agents, Michelle and Maggie, take in Anita, whom they find starving in the church. After the sisters fall asleep, Nenene gets to working on her novel.

Lee and his soldiers subdue the Paper Sisters and kidnap Nenene, leaving the Sisters with suitcases full of money to pay them for their work and convince them to leave Dokusensha alone. Meanwhile, Dokusensha attempts to forcibly implant their Perfect Language into Nenene's mind, which she resists at the cost of incredible pain. The Sisters decide to risk making a "world full of enemies" and assualt Dokusensha in order to rescue Nenene. The Paper Sisters do fine until they encounter Sonnny Wong, a more powerful Paper Master than the three of them combined.

Michelle and Anita leave Maggie behind to hold Wong's attention while they continue the search for Nenene. When the only way to get to Nenene can be traversed by the smaller Anita, Anita has to continue on alone. Meanwhile, Wendy and Joker have taken advantage of the distraction to retrieve the special books, while Junior plants bombs underneath the massive skyscrapers comprising the headquarters. Anita manages to rescue Nenene, and though Lee almost manages to subdue Anita, he repents and lets the two escape--at the cost of his own life. The bombs go off, Maggie escapes from Wong, who falls into the exploding building, and the protagonists are eventually reunited--but such was the damage of the explosion that a large portion of Hong Kong Island sinks along with Dokusensha's headquarters. Back in Tokyo, a familiar female voice leaves a brief message on Nenene's answering machine.

Joker's secretary, Wendy Earhart writes a report datas about the chronology of Mr. Gentleman and the British Library, explaining their intention to ressurect Gentleman using the special books they've collected. She recounts the I-Jin Incident and reveals that the I-Jin were originally created by the British Library. She also compares Yomiko Readman and the Paper Sisters. During Wendy's work break, Junior makes Wendy a special birthday dinner, and they share a rare friendly moment together. Later, Joker declares the collapse of Dokusensha, and he tells Wendy to look up for a girl with glassess.

The protagonists return to Tokyo, but quickly find themselves on the run, having been accused of causing the explosions in Hong Kong. After discovering Dokusensha orders naming Yomiko Readman as the possessor of the final Gentleman Book, the "Book of the All Seeing Eyes," the four manage to track Yomiko down to the National Diet Library, where she is hiding with the amnesiac Nancy. Yomiko is reluctant to greet a tearful Nenene and refuses to help them, when Joker enters in force, demanding Yomiko turn over the book to him.

Joker learns why it's foolish to attack four Paper Masters inside a library, and while the six women escape, Joker orders Wendy to execute plan "Fahrenheit 451". Thus, the British Library collects all the books in Jinbo-cho into a massive pile and sets them on fire. Witnessing this, Yomiko is in despair, and Anita, looking at the burning books, flashes back to her memory of the mysterious silhouette in the fire she remembers from her childhood. The silhouette she remembers bears a striking resemblance to Yomiko standing before the flames in Jinbo-Cho.

Wendy faces down Yomiko and friends and shoots Yomiko--when they are helped by some cover fire provided by Drake Anderson. The heroes, now seven, retreat to Yomiko's parents' home in the mountains of Saitama. That night, Junior shows up and tries to steal the book, but Nancy stops him, as she prevents his phasing ability from working on her. He then points a gun at her, and Yomiko pleades for him not to shoot--she says Nancy is his mother. In the confusion, Junior's gun goes off regardless...

Junior finds himself temporarily allied with the heroes (after Michelle keeps him from shooting Nancy), as they try to figure out the truth of the matters at hand. Yomiko hides in the attic with Nancy, too upset to talk, but later she finds the courage to confesses to the others about why she told Nancy that Junior was dead: the British Library planned to use Junior as the new vessel for the Gentleman, and distraught she had been unable to save Junior, she ran into hiding with Nancy. An upset Junior phases into the Book of the All Seeing Eye and projects a holographic recording of the events leading up the the fire: Yomiko had a fight with Joker, and after being taunted about Donnie Nakajima's fate, Yomiko temporarily loses control of herself and causes the fire. Inside the burning library, a tiny Anita appears, and her paper mastery manifests to protect herself from Yomiko's unwitting attack.

Having defeated the Mirror Man and his followers, Anita and Yomiko pursue Junior, and Yomiko shows Anita how to fly her paper plane. Junior rides in a helicopter with the drugged members of the group and threatens the pilot. When Anita and Yomiko reach the chopper, it explodes. Filled with rage and despair, Anita blames the entire situation on Yomiko, and throws the book into the helicopter's wreckage. She returns to her old school, meets Hisami to ask her for help, but Hisami does not recognize her.

Anita and Yomiko reunite with the others, forcing the British Library soldiers to stand off while they hold Joker prisoner. Meanwhile, Maggie and Nenene have taken refuge in a hotel, but Wendy finds them and tricks Maggie into believing Anita's life is in danger, forcing her to turn over Nenene in exchange for a chance to save Anita. Nenene goes willingly in order to spare Maggie any unnecessary grief.

Wendy prepares to exchange Nenene for Joker; in the meantime, Joker reveals to Anita that she was a test tube baby born in the British Library and tells her that Michelle and Maggie were brainwashed to take her in. Junior tells Michelle something similar, indicating Michelle had been altered to become a Paper Master, and Maggie reads a book given to her by Wendy containing a similar report. Wendy uses the Mirror Man to make the hostage exchange go in her favor and rescues Joker, but Drake, Nancy, Anita, and Yomiko manage to escape regardless. Days later, Joker announces British Library's plan to the world.

Yomiko and the others leave for London to rescue Nenene and stop Joker, but a distraught Anita remains behind. Anita returns to Nenene's apartment only to find Maggie and Michelle, and she tries to leave, declaring their life a lie. Michelle and Maggie help her realize that while they may have faked memories, the life they now share is real enough. The newly reformed Paper Sisters Detective Company flies to England to find Britain turned into a mythical nineteenth century landscape.

The three sisters meet with Yomiko and the others, and they spend a week searching for the British Library's secret location. They finally deduce the right place and discover Mr. Kim working for the British Library. After forcing Kim to help them infiltrate the headquarters. They split into three groups to rescue Junior, rescue Nenene, and capture Joker. The Paper Sisters successfully find Nenene, but Yomiko loses her nerve when facing down Joker. In the Special Operations base, Wendy is forced to hook Junior into the Gentleman Resurrection machine; while she is willing to do this, she asks him that if part of his own identity survives, to "feel free to take his revenge" on her.