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On the 300th anniversary of Romanov rule, Czar Nicholas II hosts a grand ball at the royal palace. During this celebration, 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 staretz. Rasputin plans to gain his revenge through a curse to destroy the Romanov family that sparks the Russian Revolution. During the storming of the palace, a servant boy helps Anastasia and Marie to escape. While Anastasia is escaping, she drops her music box in the panic. Anastasia and Marie eventually reach a moving train, but only Marie is able to get on as Anastasia trips and hits her head on the tracks, forcing Marie to leave her behind.

Ten years later, Russia is now under Communist rule; Marie, now residing in Paris, has offered a monetary reward for anyone who can return Anastasia to her. Two Russian conmen living in Saint Petersburg, Dimitri and Vladimir, decide to find a young girl to pass off as Anastasia. Elsewhere, an amnesiac, 18 year old orphan girl named Anya who owns the same necklace as Anastasia, has just left her orphanage and has decided to learn about her past, because she has no recollection of the first eight years of her life. Accompanied by Pooka, a stray dog, she heads to Saint Petersburg, and soon encounters Dimitri and Vladimir, who recruit her as their "fake" Anastasia. During the trip to Paris, the two men teach Anya how to behave like Anastasia and Anya and Dimitri realize a mutual attraction. In Dimitri's baggage, there is Anastasia's music box. 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. Bartok, his cowardly bat servant, unwittingly brings him his magical reliquary, thus restoring his old powers. Rasputin summons a legion of demons to kill Anya and complete his revenge, resulting in two failed attempts that make him realize he must kill her 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. However, 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. 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 eavesdrops on their argument and thus learns that she is a part of a con. Angered she begins to leave and is confronted by Dimitri, who begs her to believe that his intentions have changed. She does not accept this, and leaves, intending to get out of their plot. Dimitri, determined to right the situation and reunite the two women, 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.

Dimitri refuses the reward money and 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.