The year is 1916; in Saint Petersburg, Russia, Tsar Nicholas II is throwing a grand ball to celebrate the 300th anniversary of Romanov rule, while his mother, Dowager Empress Marie Feodorovna, gives her favorite granddaughter, 8-year-old Grand Duchess Anastasia a music box and a necklace reading “Together in Paris”, which serves as its key. The ball is interrupted by the arrival of Grigori Rasputin, a monk once trusted by the Russian Imperial Family, having since been cast out by Nicholas as a “traitor”. He enacts his revenge through a demonic green reliquary; summoning a curse that sparks the Russian Revolution. During the storming of the palace, Anastasia runs back to get her music box with Marie in tow, but find themselves separated from the rest of the royal family. A servant boy then arrives and rushes them out of the palace through a secret door, which is when Anastasia drops her music box in the panic, and the boy is clubbed by a soldier while covering their escape. As the two are running across a frozen river, Rasputin attempts to catch Anastasia when the thin ice breaks under him and he drowns. They eventually reach a moving train, but only Marie is able to get on as Anastasia trips and is knocked unconscious, forcing Marie to leave her behind.
Ten years later, Russia is now under Communist rule, during which Marie, now residing in Paris, has offered a monetary reward for anyone who can return her beloved granddaughter to her. Two Russian conmen living in Saint Petersburg: Dimitri, a conniving young man; and Vladimir, a former member of the Imperial Court, decide to find a young girl to pass off as Anastasia. Elsewhere, a young woman named Anya who owns the same necklace, has just left her orphanage and has decided to learn about her past, as she has suffered amnesia and has no recollection of the first eight years of her life. She then heads to Saint Petersburg, accompanied by “Pooka”, a dog she just found, and soon encounters Dimitri and Vladimir, who are struck by her resemblance to the young Grand Duchess, and thus recruit her as their “fake” Anastasia. The two men teach Anya how to behave like Anastasia during the trip to Paris, where Anya and Dimitri realize a mutual attraction, and it is discovered that Dimitri possesses Anastasia’s music box in his baggage. Anya recalls some small facts that she remembers from her past, though nobody realizes it.
Meanwhile, Rasputin is revealed to still be alive, but trapped in limbo: unable to die because Anastasia had not been killed. His cowardly servant Bartok, a bat, unwittingly brings him his magical reliquary after ten years, thus restoring his old powers. He quickly summons a legion of demons to kill Anya and complete his revenge, first by destroying the train that Anya and crew are riding on, then trying to make Anya sleepwalk overboard their ship to France, resulting in two failed attempts that make him realize he must do it in person.
The trio eventually arrive in Paris and meet Sophie, Marie’s lady-in-waiting and first cousin, who is in charge of interviewing the Anastasia lookalikes; it has become apparent though that Marie, tired of heartbreak, has declared not to hold anymore interviews. Despite this, Sophie sees Anya as a favour to Vladimir. Anya plays her part well, but when Sophie asks how she escaped the palace, Anya dimly recalls a servant boy opening a secret door… but she believes this memory to be nonsense, while Dimitri is shocked by what this signifies. Dimitri later reveals to Vladimir that he was the servant boy in her memory, meaning that Anya is the real Anastasia; nonetheless, he is saddened by this truth, because “princesses don’t marry kitchen boys.”
Sophie then arranges for Anya to encounter Marie at the Russian ballet. After the event, Dimitri attempts to introduce Anya, but the empress refuses to listen to him, having heard of Dimitri and his initial plans to con her. Anya overhears the conversation and becomes enraged with Dimitri before leaving. Dimitri later kidnaps Marie in her car and drives to the hotel where Anya is packing her things, convincing her to meet with Anya by giving her the lost music box. Upon meeting Anya at first, Marie remains guarded until the girl suddenly begins to remember personal childhood moments. As they sing the lullaby the box plays, Marie finally realizes the truth, and the two reunite at long last.
At a later meeting, Marie is moved to find that Dimitri is refusing the reward money for returning Anya, despite being the same servant boy who saved them years ago – he leaves. Marie eventually tells Anya of Dimitri’s actions at the ball, making her realize her error. When Pooka suddenly bounds for the garden maze, Anya runs after him and is trapped. Rasputin finally reveals himself to her and tries to kill her on the Alexander Bridge over an icy Seine River. Dimitri returns to save Anya, and in the ensuing fight, Anya manages to destroy Rasputin’s reliquary by crushing it under her foot, causing him to disintegrate into dust.
Dimitri and Anya reconcile, sending a farewell letter to Marie and Sophie. The film ends with Anya and Dimitri sailing away on a boat with Pooka, before sharing a passionate kiss. Bartok, looking down at the spectacle, suddenly encounters a female bat and shares a kiss with her as well.