The act of posing as a female figure unmasks Einar’s lifelong identification as a woman, whom he has named Lili Elbe. This sets off a progression, first tentative and then irreversible, of leaving behind the identity as Einar, which he has struggled to maintain all his life. This takes place as both Lili and Gerda relocate to Paris; Gerda’s portraits of Lili in her feminine state attract serious attention from art dealers in a way that her previous portraiture had not. It is there that Gerda tracks down art dealer Hans Axgil (Matthias Schoenaerts), a childhood friend of Lili (Hans had been the first boy who had ever kissed him as Lili). Hans and Gerda’s mutual attraction is a challenge, as Gerda is navigating her changing relationship to Lili; but Hans’ long-time friendship with and affection for Lili cause him to be supportive of both Lili and Gerda.
As Einar’s continued existence as his male self becomes too much for Lili, she starts to seek help from psychologists, but none yields any result, and, in one instance, almost leads her into being committed to an asylum. Eventually, at Hans’s recommendation, Lili and Gerda meet Dr. Kurt Warnekros (Sebastian Koch). Dr. Warnekros explains that he has met several people like Lili, who are physically male but identify as female, and proposes a new, innovative and controversial solution: male to female sex reassignment surgery. This would entail a two-part procedure that involves first removing Lili’s external genitalia and then, after a period of recovery, fashioning a vagina. He warns them that it is a very dangerous operation that has never been attempted before, and Lili would be one of the first to undergo it. Lili immediately agrees and, soon after, travels to Germany to begin the surgery. Unfortunately, her eagerness to shed the vestiges of the male anatomy leads her to rush the sequence of procedures, and Lili eventually dies of complications from the surgery. The movie ends with Gerda and Hans on a hilltop back in Denmark, in front of the five trees Lili had painted way back in her male life as a painter. The scarf that Lili had originally given Gerda, and that had subsequently been given back and forth several times, is carried away on the wind, dancing.