In 1916 Saint Petersburg, at a ball celebrating the Romanov tricentennial, Dowager Empress Marie gives a music box and a necklace inscribed with the words “Together in Paris” as parting gifts to her youngest granddaughter, 8-year-old Grand Duchess Anastasia. The ball is suddenly interrupted by Grigori Rasputin, a sorcerer and the former royal adviser until he was exiled for treason. Seeking revenge, Rasputin sells his soul in exchange for an unholy reliquary, which he uses to curse the Romanovs, sparking the Russian Revolution. As revolutionaries siege the palace, Marie and Anastasia escape through a secret passageway with the aid of 10-year-old servant boy Dimitri. Rasputin confronts the two royals outside on a frozen river, only to fall through the ice and drown. The pair manage to reach a moving train; but, as Marie climbs aboard, Anastasia falls, hitting her head on the platform and subsequently suffering amnesia.
Ten years later, Russia is under communist rule and Marie has publicly offered 10 million rubles for the safe return of her granddaughter. Dimitri and his friend/partner-in-crime, Vlad, search for an Anastasia look-alike to bring to Paris so they can collect the reward. Elsewhere, an 18-year-old Anastasia–now called “Anya”–leaves the rural orphanage where she grew up. Accompanied by a stray puppy she names “Pooka,” she decides to head to Paris, inspired by the inscription on her necklace, but finds she is unable to leave Russia without an exit visa. An old woman advises her to see Dimitri at the abandoned palace; there, Anya experiences visions of her past. The two men are impressed by Anya’s resemblance to the “real” Anastasia, and decide to take her with them to Paris.
Rasputin’s albino bat minion, Bartok, is nearby and notices his master’s dormant reliquary suddenly revived by Anya’s presence; it drags him to limbo, where he finds Rasputin has survived. Enraged to hear that Anastasia escaped the curse, Rasputin sends his demonic minions from the reliquary to kill her. The trio departs Saint Petersburg by a train, but are forced to jump off when Rasputin’s demons take over the train engine by overheating it and separating it and its baggage car and speeding it up and cause it to fall off a bridge they blow up and explode. While journeying to a ship to take them to France, Dimitri and Vlad educate Anya on her family’s history and court etiquette. On the ship, Dimitri and Anya share a dance and begin to fall in love. That night, Rasputin’s demons make Anya dream about her family and lure her into nearly sleepwalking off the ship before being narrowly rescued by Dimitri. After two failed attempts, Rasputin and Bartok travel back to the surface to kill Anya themselves.
The trio eventually reach Paris and go to see Marie, who has given up the search after meeting numerous imposters. Despite this, Marie’s cousin Sophie quizzes Anya to confirm her identity. Though Anya offers every answer taught to her, Dimitri finally realizes she is the real Anastasia when she (without being taught) vaguely recalls how he helped her escape the palace siege. Sophie, also convinced, arranges a meeting with Marie at the Paris Opera House. There, Dimitri tries to establish an introduction but Marie refuses, having already heard of Dimitri’s initial scheme to con her. Anya overhears the conversation and angrily leaves. Dimitri later abducts Marie in her car to force her to see Anya; finally convincing her when he presents the music box Anastasia dropped during their escape. As Marie and Anya finally converse, Anya regains more memories. Opening the music box and singing their lullaby, Marie realizes that Anya is indeed Anastasia and the two are joyfully reunited.
Marie offers Dimitri the reward money the next day, recognizing him as the servant boy who saved them; to her surprise, he refuses it and leaves to return to Russia. At Anastasia’s return celebration, Marie informs her of Dimitri’s gesture, leaving Anastasia torn between staying or going with him. Pooka suddenly runs off; Anastasia chases him to the Pont Alexandre III, where she is trapped and attacked by Rasputin. Dimitri returns to save her, but is soon injured and knocked unconscious. In the struggle, Anastasia manages to get hold of Rasputin’s reliquary and crushes it under her foot, avenging her family as Rasputin disintegrates and dies.
In the aftermath, Anastasia and Dimitri reconcile; they elope, and Anastasia sends a farewell letter to Marie and Sophie, promising to return one day. Bartok shares a kiss with a female bat before bidding the audience farewell.