Kazuya Kujo is an exchange student from Japan. While exploring the library he encounters Victorique de Blois. While talking her extravagant brother Grevil arrives and questions Victorique through Kujo about a locked room murder. Victorique sets her mind to the task and comes up with an improbable but entirely logical answer.

Posing as the murdered Soothsayer, Roxane and her servant, Victorique and Kujo have boarded the Queen Merry. Once on board they discover they have fallen into another mystery, this one with deadly intent towards everyone.

The trap closes and the architect behind it is revealed or is he? Victorique picks up on a larger scheme that set much larger things in motion. The question is are the still in motion to this day?

Kazuya witnesses the bizarre beheading of a man riding a motorcycle. While a suspect matching the description Victorique surmised is arrested a new girl joins Kazuya’s school who also matches the description.

The case of the beheaded man is brought to a close after Victorique reveals the true identity of the new student at the school.

Kazuya is stumped by the disappearance of a valuable plate from a local bazaar. At the same time he sees an advertisement in the paper call for all “Descendants of the Gray Wolves” to return to their ancestral home. After telling Victorique about it she insists on going to the town immediately.

Victorica and Kujo explore the "Village of the Gray Wolves" where her mother lived in search for clues to prove her innocence, but Victorica gets disappointed when she uncovers the truth and figures that she lacks the means to clear her name. To complicate matters, two of the tourists who were visiting the village with them are killed among strange circumstances.

Victorica manages to find the culprit behind the recent deaths at the village and to clear her mother's name by exposing the woman who framed her. However, when the woman attempts to escape, she starts torching the entire village, and Kujo must confront her while protecting Victorica with his life.

Victorica gets a fever as Kujo sets out alone for some errands in Sauville. While searching for a souvenir for his sister, he meets a girl among a pile of mannequins. The girl asks for help, but when he gets back to the department store with the Inspector, she is nowhere to be found. Kujo calls Victorica by phone to ask her help, but the call is cut short as he is taken away.

Kujo encounters the same girl he met at the department store, and with the help of hers and a bright homeless boy, he manages to put the police back on the case. Kujo and Grevil then ask Victorique's opinion about the store, just to find that she already had made some research about it, and she comes with a plan to expose the culprits.

Jaqueline, an old friend of Grevil's, pays a visit to the Academy to make a donation and has a sudden encounter with Victorique at the Library Tower. There, she tells the story of a mysterious incident from the past where she was falsely accused of murder, unaware about its connection with both Victorique and the reason why Grevil has started bearing his unusual hairstyle.

Everybody in school are preparing for there summer vacation. Kujo has turned down his vacation trip with Avril to stay with Victorique. Kujo has flash back of his past of why he left japan, while relaxing on a tree. When Kujo went into the academy, Victorique wanted to climb the tree Kujo was on and gets stuck in the tree forcing Kujo to save her. Kujo then chills at Victorique's house while it rains, but she spills tea all over her kimono and forcing Kujo to clean it up. The scene ends with Kujo remembering to to buy sweet for Victorique.

Kujo and Avril explore one of the school's towers and Avril figures that it is related to the legend of Leviathan, an alchemist who lived there decades before. Victorique stumbles on a pop-up book containing a cryptic message aledgely from Leviathan himself and when a death occurs at the top of the tower, she decides to investigate by herself.

Victorique is dragged by her teacher to her classroom and is introduced to the rest of her classmates. Avril tries to bring her attention but she gets angry on her instead. Kujo demands Victorique to apologize to her, and when she refuses, he sets with Avril to keep investigating the Leviathan case without her help. Meanwhile Victorique has an encounter with Brian Roscoe, a friend of the victim's, on the top of the clock tower.

Kujo inquires Brian Roscoe regarding his connection to Victorique and her mother, but he only warns him to beware of her father instead. Meanwhile, Victorique succeeds to unlock the secrets behind Leviathan, the clock tower and the truth about her own origin.

Victorique's father has her taken from the academy to a convent known as "Beelzebub's Skull" in Lithuania. Kujo learns about her whereabouts from Grevil and takes a train going there to look for her. Guided by a woman who resembles a lot like her, Kujo manages to find where Victorique is held and learns from her that the woman is most likely her mother, Cordelia.

Victorique reveals to Kujo that her father brought her to the convent in order to bait out Cordelia and Brian. As the two escape, they become separated by an illusion. Victorique encounters Brian, who reveals that he is planning to stop her father and the Academy. Meanwhile, Kujo runs into Cordelia, who entrusts him with a ring and some words of encouragement for her daughter, then Marquis Albert de Blois himself. Albert attempts to force Kujo to surrender Victorique to him, but Kujo refuses and leaves. The floodgates shielding the convent are opened by a time-release trap set by Albert, flooding the entire area, and Kujo barely escapes with Victorique.

Having escaped from the flood, Victorique, Kujo and the rest of the passengers of the Masquerade Express find themselves involved into a bloody contest for an elusive item that can shake the balance of power between the Academy and the Ministry of Occult.

Kujo leaves to the capital to find a present to Victorique's birthday which coincidentaly is on christmas day. Meanwhile, Victorique receives a message from her mother and starts looking for Kujo without success until she is summoned by her father and taken by Grevil to the capital to solve the greatest mystery of the country, which involves its previous queen, Coco Rose, whose life is being reenacted in a play at the Phantom Theater.

Kujo rushes to catch Victorique, summoned again by her father, but she disappears once more. The Inspector explains she cannot leave until she solves the Coco Rose case, about a queen found beheaded in her chambers. Kujo gathers the Fragments of Chaos she cannot assemble, uncovering that Cordelia was once a showgirl who vanished, along with a woman resembling Coco Rose. During his investigation, Kujo meets Brian Roscoe, who leads him back to the theatre where Victorique is held. Reunited, her father allows her to leave and assemble the Fragments. Prompted by Kujo’s findings, Victorique begins her investigation at the grave of Nicole Le Roux, the woman resembling Coco Rose.

Upon investigating the grave of a woman with a striking resemblance to Queen Coco Rose, Victorique manages to put together the truth behind her mysterious demise. The truth of the Coco Rose case and the disappearance of Nicole Lulu is made clear, and Albert frees Victorique when she is unable to conclusively identify the murderer. On the way home to the Academy, Victorique and Kujo encounter a seemingly ordinary couple who are actually the still-living Coco Rose and her son fathered by Leviathan. Cordelia watches over them as they arrive home, and is soon joined by Brian and then a man who seems to be Brian's twin.

Kujo is enjoying Christmas together with Victorique when he is taken by force from the Academy as King Rupert declared that all foreign citizens should be sent back to their home countries in spite if the imminent conflict in Saubure. However, Kujo manages to escape and returns to the Academy eager to meet Victorique again, unaware that he became a hostage in Albert's hands as a mean to ensure her cooperation with his plan.

By Spring 1925, Albert's plan is complete: Kujo has been deported, and Victorique imprisoned in Sauville. Albert exposes Jupiter Roget as a Gray Wolf, drives him out, and convinces King Rupert to ally with Germany. In Winter 1925, Kujo joins the Japanese military, and Albert becomes Sauville's Prime Minister, having Grevil bring Victorique to the ceremony to display his power. However, Cordelia had switched places with Victorique, revealing Albert's crimes to the nation. When one Brian Roscoe twin stages a terrorist attack, Cordelia fights Albert with knives, kills him, but is slain by his minion. Meanwhile, the other Brian, who has taken Victorique away, tries to kill her to erase Cordelia's "pain."

After attempting to kill Victorique, Brian Roscoe falls from a cliff and is gravely injured, while his brother dies holding Cordelia's hand. Victorique saves him, and they are found by Grevil, who lets them escape. On a departing boat, Brian tells Victorique that Cordelia was the mother he and his brother always wanted, urges her to live for her mother's sake, and passes away. Victorique’s hair turns silver, helping her evade capture. Jupiter Roget brings Kujo’s letters, and after the war, the academy reopens with Grevil returning to his old hairstyle. Jupiter informs the king of Cordelia's sacrifice, and the king seeks his help again. Avril sends a bottle letter to Kujo and Victorique, which returns. Ambrose finishes reading the Monstre Charmant, whose characters bid farewell as the kingdom of Sauville is symbolically replaced by a new dawn. In Spring 1929, Kujo returns to Japan to reunite with Victorique.