Francis, an intelligent and cynical cat, is moved to a gloomy, dilapidated house with his owner Gustav Löbel, an archaeologist and erotic novelist. During Francis' exploratory tour of the house, he discovers a chemical odor emanating from the topmost floor, as well as the fresh corpse of a cat who had been killed by a targeted bite. At the scene of this murder, Francis meets and befriends Bluebeard, a half-blinded, foul-mouthed Manx. Soon, Francis discovers another body and the fact that his house's top floor is the meeting site of a sect of cats led by Joker; the members of the sect worship an entity named Claudandus and perform ritualistic suicide by throwing themselves in an electric current. When Francis' cover is blown, he is chased through the city's rooftops. He escapes through a skylight and meets a blind cat named Felicity, who informs Francis that Claudandus was a cat who lived in their area years ago, and was tortured relentlessly by humans. He is hailed as a savior among the local cats, who to this day pray for him. Felicity also reveals that the victims of the murders have consistently been sexually-excited male cats who have conversed with an urgent, convicted and persuasive voice they were all acquainted with. The next day, Bluebeard takes Francis to Pascal, an elderly and tech-savvy cat who has taken to meticulously maintaining a list of feline deaths in the area, through which Francis learns that Felicity is the latest victim. That night, Francis is haunted by a nightmare in which Gregor Mendel leaves him with riddles. During a rodent hunt, Francis discovers a video recording that documents the top floor's previous use as an experimental laboratory that was devoted to the research and development of a tissue adhesive that would close wounds in an instant. The test subjects largely consisted of stray cats. However, the serums usually failed, causing the animals to suffer painful deaths. The one cat who survived the experiments was christened by the lab's technicians as "Claudandus", Latin for "He who should or must be sealed". The video recording ends with the lead researcher, Professor Julius Preterius, attempted to release Claudandus from his cage, believing to be able to speak to him. The murders seem to point to and are taken credit by a large and aggressive neighborhood cat named Kong. However, while escaping Kong and his goons, Francis comes across the disemboweled remains of a female pregnant cat named Solitaire. Kong, who had mated with Solitaire, is devastated over her and his unborn kittens' deaths, leaving the trail cold. Francis has another dream in which a brightly colored cat who calls himself "Felidae" persuades Francis to join him on a long, wonderful journey. Francis wakes to the calls of a female cat in heat, whose breed he doesn't recognize. She replies to the question of her breed with a cryptic answer, saying that it is "old and new". The query of her name is similarly stonewalled, so Francis unquestionably complies to the amorous female's insistence that they copulate. An exhausted Francis tells Bluebeard of the she-cat he met, and how she looked different from them. Bluebeard reveals awareness of her breed, and states that they are in many ways different from them. Not only have they been recently been taken in by humans as household pets (to which Bluebeard claims to be a death wish), but for some reason, they lack the same healthy trend to domestication found in most cats. This makes them more feral and more solitary, to which Bluebeard considers makes them "dangerous". Francis gradually traces the neighborhood cats who descended from the strays involved in the experiments and is confronted by Pascal, who reveals himself as Claudandus. He reveals that he killed Professor Preterius shortly after he released him from his cage and was taken by one of the researchers, during this time he learned about the Mendel Genetical Theory and plans to create a breed of genetically engineered cats to wipe out humanity. The murdered cats, now including Joker, were deemed unworthy of breeding with the pure females that Claudandus had engineered. An additional obstacle in Claudandus' plot is the fact that he is terminally ill with stomach cancer. Although Claudandus deems Francis an ideal successor, Francis defies Claudandus' ambition and attempts to delete the data that Claudandus had gathered. The ensuing fight between the two results in a fire, where Francis eventually disembowels and kills Claudandus and flees the scene with an injured Bluebeard. Following these events, Francis is reunited with Nhozemphtekh and they walk home.
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