In 1916, Tsar Nicholas II hosts a ball at the Catherine Palace to celebrate the Romanov tricentennial. His mother, the Dowager Empress Marie Feodorovna, is visiting from Paris and gives a music box and a necklace inscribed with the words “Together in Paris” as parting gifts to her eight-year-old granddaughter, the Grand Duchess Anastasia. The ball is suddenly interrupted by Grigori Rasputin, a sorcerer who was banished by the Tsar for treason. Rasputin had then sold his soul in exchange for an unholy reliquary, which he uses to cast a curse on the Romanov family in revenge, sparking a revolution that forces them to flee the palace. Only Marie and Anastasia are able to escape, thanks to a young servant boy named Dimitri, who shows them a secret passageway in Anastasia’s room. Rasputin confronts the two royals outside, only to fall through the ice and drown. The pair manage to reach a moving train, but only Marie climbs aboard while Anastasia falls, hitting her head on the platform.
Ten years later, Russia is under communist rule, and Marie has publicly offered ten million rubles for the safe return of her granddaughter. Dimitri and his friend and partner Vladimir thus search for an Anastasia lookalike to present to Marie in Paris and collect the reward. Elsewhere, Anastasia, now under the name “Anya”, leaves the rural orphanage where she grew up, having lost her memory prior to arriving there. Accompanied by a stray puppy she names “Pooka”, she turns down a job at a fish factory in favor of going to St. Petersburg after her necklace inspires her to seek out her family in Paris. In the deserted palace she encounters Dimitri and Vladimir, who — impressed by her resemblance to the “real” Anastasia — decide to take her with them.
Bartok, Rasputin’s albino bat minion is nearby and notices his master’s dormant reliquary suddenly revived by Anastasia’s presence; it drags him to limbo, where Rasputin survives. Enraged to hear that Anastasia escaped the curse, Rasputin sends demonic spirits from the reliquary to kill her; despite two attempts, the trio manage to (unwittingly) foil him, forcing Rasputin and Bartok to travel back to the surface.
Anastasia, Dimitri, and Vlad eventually reach Paris and go to meet Marie, who refuses to see her, having been fooled numerously before by impostors. Despite this Sophie, Marie’s cousin, quizzes Anastasia to confirm her identity. Dimitri and Vladimir had taught Anastasia all the answers, but when Anastasia independently (though dimly) recalls how Dimitri saved her ten years ago, the two men finally realize that she is the real Grand Duchess. Dimitri, however, insists they do not reveal this truth to Anastasia. Sophie, convinced as well, arranges for Anastasia to meet Marie after a Russian ballet. However, Marie wants nothing to do with Dimitri, having heard of him and his initial scheme to trick her. Horrified that Dimitri was using her, Anastasia storms out. Dimitri, having fallen in love with Anastasia, manages to change Marie’s mind by presenting her with Anastasia’s music box, which he had found after their escape. Anastasia’s memory returns upon meeting Marie, and the two women are reunited at long last.
The next day, Marie offers Dimitri the reward money, but to her surprise he refuses it and leaves for Russia, convinced that he cannot be with Anastasia. That night, at Anastasia’s return celebration, Marie informs her of Dimitri’s gesture and leaves her to her thoughts. Anastasia then wanders through a garden and onto the Pont Alexandre III, where she is trapped and attacked by Rasputin. Dimitri returns to save her, but is injured and knocked unconscious. Anastasia manages to kill Rasputin by crushing the reliquary under her foot. With Rasputin’s soul having been tied to the object, he promptly dies and turns to dust.
Afterwards, Dimitri and Anastasia reconcile; the two then elope and Anastasia sends a farewell letter to Marie and Sophie, promising to return someday. The film ends with the couple sharing a kiss as they sail out of Paris with Pooka, while Bartok falls in love with a female bat who kisses him.