The film opens in 1938. Dominic Matei (Tim Roth) is a 70-year-old professor of linguistics. On the eve of World War II, Dominic attempts to visit the Café Select but is denied access due to wearing his pyjamas. Dominic realises that he is getting no younger, and has essentially failed his aim in life – to fully discover the origin of human language. His tireless labours have condemned him to a solitary existence, often spent pining after Laura (Alexandra Maria Lara), the love of his youth. Intent on committing suicide, Dominic travels to Bucharest, the city where he and Laura met at university. He is struck by lightning. In hospital, he is initially diagnosed by Professor Stanciulescu (Bruno Ganz) to be dying of his burns. However, Stanciulescu is startled when his patient regenerates into a much younger man. The Professor helps Dominic out of the hospital so as to continue studying him. Shortly afterwards, Romania is occupied by the Nazis, whose interests are aroused by Stanciulescu’s miracle patient.
While residing at the Professor's home, Dominic realises that he possesses strange capacities. He begins to experience multiple planes of reality, blurring his perception of whether he is awake or asleep. He mistakes the “Woman in Room Six” (Alexandra Pirici) for an erotic fantasy – when in reality, she is a Nazi spy. During his nights together with the Woman, Dominic discovers he has an unnatural talent for languages after they communicate effortlessly in French, German, and Russian. As his abilities progress, Dominic becomes aware of an “other” self who speaks to him in mirrors and dreams. This alternate persona serves as the voice of his condition, claiming to exist outside of space and time. When Dominic asks for proof, the “other” obliges by bringing him two roses which materialise out of nowhere. Unbeknownst to Dominic, Stanciulescu has witnessed the event and overhears his friend ask himself “Where do you want me to place the third rose?”. This gives the Professor great concern and understanding for the Nazis’ designs upon Dominic. A Third Reich programme led by Doktor Josef Rudolf (André Hennicke) has recently confiscated his research and is unsuccessfully attempting to duplicate the lightning. Stanciulescu persuades Dominic to escape from Romania, aided by anti-Nazi sympathisers. While on the run, Dominic discovers he now possesses the knowledge to forge passports and conceal his identity. Thanks to the Nazi confiscation of research, Dominic’s existence has essentially been erased from the records. Later, he is saddened to learn that the Professor has died in a plane crash.
Living like a spy, Dominic eventually arrives in Switzerland. Unfortunately, the Woman in Room Six has managed to pick up his trace, leading to a confrontation between Dominic and Doktor Rudolf in an alleyway. The doctor argues that Dominic’s existence supports the Nazis’ ideal of the superman, and that the coming nuclear warfare can only be survived by a superior species of man. In the background, the “other” Dominic confirms this to be the case. However, Dominic himself refuses to cooperate, forcing the doctor to pull a gun on him. The Woman is shot defending Dominic, provoking him to telekinetically manipulate Rudolf into shooting himself. The war ends but Rudolf’s fears about nuclear armament are realized. Dominic resumes a normal existence, during which he continues his research. Realising that he has been transformed into a human of the future – thus giving him knowledge of the fate of mankind – he develops a secret language for his audio diary, to be deciphered by a supercomputer in the year 2010 – long after the nuclear apocalypse.
Many years later, Dominic encounters a girl named Veronica (Alexandra Maria Lara) while hiking in the Alps. The “other” reveals her to be the reincarnation of Laura. When the mountains are hit by a violent storm, Dominic rushes to her rescue. He finds her huddled in a cave, chanting in Sanskrit, which he greets her with to gain her trust. During her stay in hospital, Dominic finds that Veronica now identifies herself as “Rupini”, the daughter of a wealthy family in India who were among the first disciples of the Buddha and follower of Candrakīrti. While the doctors assume she is suffering from amnesia and delusion from the incident, he suspects that she may now be suffering from a condition similar to his own and calls the Roman College of Oriental Studies for aid. Led by Professor Giuseppe Tucci (Marcel Iures), the scholars confirm that Rupini was a real person, who went to a cave many centuries ago to meditate on Enlightenment. Since the cave’s location is unknown, the scholars agree to fund an expedition to find the cave in India, hoping that Veronica’s past self will guide them. Dominic volunteers to accompany them under the alias “Martin Audricourt”. The venture proves a success when a local holy man recognises “Rupini” and directs her to the place of meditation. While investigating the cave, Dominic finds the bones of the original Rupini. After this discovery, Veronica becomes herself again and no longer speaks Sanskrit. Some time passes and she begins to fall for Dominic.
The couple elopes to Malta, where they live happily together – until Dominic tells a sleeping Veronica that he has always loved her. This causes Veronica to writhe on the bed as if possessed and begin chanting in a language even he does not understand. The “other” appears to him and explains that she is speaking in ancient Egyptian, having travelled further back along the path of her past selves. Over the next two weeks, Dominic and the “other” learn how to control this state in Veronica, leading her to regress even further back in time and speak languages such as Babylonian, Sumerian, Proto-Elamite and previously unknown tongues. However, Veronica's health begins to decline from exhaustion, and Dominic declares that he cannot continue these sessions – or even being close to Veronica, since his proximity is accelerating her age. The “other” disagrees and urges him to find the Ur-Language, which would complete his life's work. Dominic tearfully explains everything to Veronica and leaves her weeping, begging for him to stay. In 1969, Veronica departs from a train with two children in Switzerland. Without being noticed, Dominic takes a snapshot of her and begins to cry when she passes without recognizing him. Despairing, he returns to the town where he taught as a professor. His alter ego appears to him and reveals the truth about the future – nuclear warfare will unleash an electromagnetic pulse, giving birth to a new and more powerful human species, of which Dominic is but the first member. Veronica symbolised the dawn of man, and he stood for the dusk. Dominic is outraged at the idea of sacrificing millions of lives in the name of evolution and shatters the mirror. The “other” is completely taken off guard and slowly vanishes, all the while yelling in an unknown language.
The film comes full circle when Dominic returns to the Café Select to clear his thoughts. While there, he encounters all of his old colleagues, who are long dead. As more friends from his past join him and offer warm greetings, Dominic becomes more agitated and begins to age, complaining that this is a dream of a dream of a dream. He mumbles that should he ever solve the "worry that we all share," he will tell them the answer. Dominic stumbles out of the room and journeys back into the snowy winter night. In the morning, townsfolk find his aged body, lying dead at the bottom of a staircase. They search his passport, but find only the younger alias of “Martin Audricourt”.
In the final scene, Veronica’s voice is heard echoing “Where do you want me to put the third rose?” – the rose appears in Dominic’s lifeless grasp.