In 1944, soon after the Soviet Red Army had taken Lithuania from Germany, the Nazis launch a counter-assault. During this time, eight-year-old Hannibal Lecter, his younger sister, Mischa, and their parents quickly escape to the family's hunting lodge. After the Nazis take over Lecter Castle, six Lithuanian militiamen, who want to join the Waffen-SS, are told to prove their worth. Grutas orders them to kill the Lecters' Jewish cook. They also threaten another servant of the Lecter household, asking him if he was a Gypsy or a Jew. As this happens, the Soviet Red Army begins launching attacks to retake the area.
A Soviet tank crew stops at the Lecters' lodge, telling the Lecters to stand away from the house while they get some water. The Soviet soldiers allow Hannibal and Mischa to stay within the lodge, where it is warmer. The Soviet tank is then spotted by a German Stuka bomber, which sparks a firefight. The bomber is shot down by the tank, but subsequently crashes into it, and the ensuing explosion kills everyone who was outside. The Lithuanian militiamen then loot Lecter Castle as the Soviet Red Army draws nearer. The advancing Soviet army forces the Nazi militiamen to hide out in the woods, where they happen upon the Lecter lodge. Finding no other food in the bitterly cold Baltic winter, they murder and cannibalize Mischa in front of Hannibal, who escapes and is found half-dead by Soviet soldiers.
Eight years later, Lecter once again lives in Lecter Castle, which has been turned into a Soviet-run orphanage. His co-residents are under the impression that he has been rendered mute by his childhood trauma. After exacting his revenge on a bully at the orphanage and retrieving letters from his uncle, Lecter escapes the castle orphanage, gets through border controls and goes to live in Paris with his aunt, Lady Murasaki. She manages to get him to speak and begins teaching him the arts of flower arrangement, martial arts, and ancestor worship.
At a local market, a butcher and former Vichy collaborator, makes racist remarks about Lady Murasaki and sexually harasses her, causing Lecter to fly into a rage and attempt to beat the man to death. The butcher later goes fishing and is disrespectful when Lecter turns up to request an apology. Lecter slices the butcher's stomach, arm and back with a katana samurai sword, and then decapitates him. That same evening, he is questioned about the butcher's murder by Inspector Popil, a French detective who also lost his entire family during the war. While her protégé is being interrogated, Lady Murasaki places the butcher's head outside the headquarters with a swastika carved into his forehead, thus absolving Lecter of suspicion; but Popil is not convinced that Lecter is innocent.
Lecter soon becomes the youngest person ever admitted to medical school in France. He receives a working scholarship, where he is given a job preparing cadavers. One day, Lecter witnesses a condemned war criminal receiving a sodium thiopental injection to force him to recall repressed memories about his crimes. In an attempt to recall the names of those responsible for his sister's murder, Lecter injects himself with the solution while listening to Glenn Gould's recording of the Goldberg Variations. His subsequent recollection reveals that Pot Watcher had the dog tags of the other men who killed Mischa, and was subsequently killed as the advancing Soviet forces bombed a part of the lodge, which collapsed on top of him. Lecter reasons that the dog tags should still be in the ruins of the lodge.
Lecter returns to Lithuania in search of the dog tags, as well as his sister's remains. Because he crosses the Soviet border, a list containing his name draws the attention of Dortlich, who is now a Soviet border patrol officer. Lecter excavates the ruins of the lodge and unearths the dog tags of the deserters who murdered Mischa. Dortlich tries to kill him, but Lecter gets the upper hand and incapacitates him. After he buries Mischa's remains, Lecter tortures Dortlich into revealing the whereabouts of his accomplices. He then decapitates Dortlich with an elaborate horse-drawn pulley lubricated with mayonnaise. Having killed the first of the men responsible for slaughtering and eating his sister, Lecter returns the favor in kind by cannibalizing Dortlich, making a meal out of his cheeks and wild mushrooms.
One of the pieces of information that Lecter had managed to extract from Dortlich was the location of one of the other men, Kolnas. At a restaurant in Fontainebleau, Lecter encounters Kolnas's young daughter, who, he notices, is wearing a bracelet that Kolnas had stolen from Mischa. Hannibal then distracts her while he slips Kolnas' dog tag into her pocket, which Kolnas subsequently discovers. Lady Murasaki tries to persuade Lecter to spare him, for the sake of his children.
Dortlich's murder, along with Kolnas' discovery of his own dog tag, puts the rest of the group on alert. Grutas, now a sex trafficker, dispatches a second member of the group, Zigmas Milko, to kill Lecter. Milko sneaks into Lecter's laboratory at night with a gun, but Lecter, anticipating an assassination attempt, tricks him with the aid of a cadaver and knocks him out with an injection. Lecter locks Milko in the cadaver tank and leaves him to drown in the embalming fluid just as inspector Popil enters the laboratory.
Popil questions Lecter about Dortlich's murder, but is again unable to prove Lecter's guilt. Popil, dropping all pretences, then tries to dissuade him from killing the rest of the gang and offers to grant him immunity if he helps the police to locate Grutas, who is still a wanted war criminal. After Lecter relays all of the details of his past to the police, Popil remarks to his assistant that Lecter lost all of his humanity when Mischa died, and that when they do arrest Grutas, that he will have Lecter locked up in an asylum as well. That night, Lady Murasaki reveals her romantic feelings to Lecter and begs him to stop, but Lecter says that he made a promise to Mischa. He plants a time bomb in Grutas' home and attacks him in the bath. A maid alerts Grutas' bodyguards, but just as they are about to kill him, Lecter's bomb goes off and he manages to escape.
Grutas kidnaps Lady Murasaki to use her as bait. Lecter recognizes the sounds of Kolnas's ortolans from his restaurant in the background. Lecter goes to the restaurant and manipulates Kolnas into believing that he, Lecter, had kidnapped his children and had already injured them, forcing Kolnas to give up the location of Grutas' boat. Lecter then calls Kolnas' home and hands over the phone to him. Panicked, he shouts at his wife to check on the children, to which she complies and returns to tell him that the children are safe in their beds. Lecter then lays his gun down on the stove between him and Kolnas, saying that he will leave Kolnas alive for the sake of his family. Realizing that he had been duped, Kolnas angrily goes for the gun anyway, but Lecter is ready for this and impales him through the head with his tantō.
Lecter goes to the houseboat. Just as he is about to untie Lady Murasaki, Grutas shoots him in the back. Grutas then proceeds to molest Lady Murasaki in front of Lecter, who then takes out the katana from his back-sheath, which had shattered when blocking the bullet, and slashes Grutas's Achilles tendons with it, crippling him. Hearing Hannibal say he must kill them because they ate his sister, Grutas taunts Lecter with the fact that he too had consumed her in a broth fed to him by the deserters, and that he was killing them to keep this fact secret. A livid Lecter then carves his sister's initial, M, into Grutas's chest and proceeds to eat him alive, starting with his cheeks.
Lady Murasaki flees in horror. Lecter tries to tell her that he loves her, but she replies that there is nothing left in him to love. The houseboat is then incinerated, but Lecter, assumed by Popil to be killed in the blast, is seen by Lady Murasaki emerging from the water on a nearby wooded shore. Lecter is then shown to be hunting down the last member of the group, Grentz, in Canada. Stopping in at a general store run by Grentz, Lecter claims to be eager to collect a big trophy. He then drops Grentz' dog tag on the counter, which he then picks up and looks up at Lecter in horrified realization. The final shot is of Lecter driving away with a children's song (a favorite of Mischa's) being sung in the background.
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