In the near future, access to cities is restricted and regulated through the use of health documents, known as "papeles." The dystopian society is regulated by various "codes," and the code of the movie title prohibits "genetically incestuous reproduction." William Geld, an insurance fraud investigator, is sent to Shanghai, where he falls in love with Maria Gonzalez, a woman who forges "papeles." They have an affair, and after he returns from a trip abroad, he discovers that she's missing. Her apartment is abandoned and the only clue is a medical clinic appointment. He visits the clinic and, using his empathic abilities, learns that Maria was pregnant and that the pregnancy was terminated due to a violation of Code 46. William knows that this means Maria is somehow genetically related to him, but he has no idea how. He finds Maria and discovers that her memory has been erased. She eventually remembers who he is as he's trying to return abroad to his wife and family. William also reveals to Maria that she's been given a virus that induces an adrenaline rush in response to physical contact with the person who brought about the Code 46 violation. They still have sex, and Maria enters a somnambulistic state, reporting the Code 46 violation. Maria is punished by a tribunal, and William is able to return to his wife and children with his memory erased.