The final occupant of room 2046 is the hotel owner's daughter, played by Faye Wong. Previously she had appeared in the film "Chungking Express"(1994) with Tony Leung. She is passionately in love with a Japanese, Takuya Kimura. In real life he is a pop singer and teenage heart throb. Her father objects to this affair, and when he returns to Japan, she stays in Hong Kong. Faye suggests that Tony writes a science fiction novel based on her own life. In the novel, she is a humanoid living in the year 2046. Her boyfriend tries to persuade her to leave 2046, but she is unable to express any emotions, and is trapped in this time.

Wong Kar Wai does not tell the story in a linear manner. Time is shuffled like a pack of cards, and sometimes it is fast forwarded in a logarithmic manner. One travels to the future to find one's past.

The central theme of the film is about memories. The feeling of deja vu is particularly acute if you have seen any of Wong Kar Wai's previous films because he reprises the actors and recreates some of the visual imagery. This plays on the audience's memory. But things are not quite the same in the present day. Thus when Tony recognizes Carina Lau, who played the role of Lulu in "Days of Being Wild" (1991), she has changed her name, and does not remember him initially. Memorable songs like Chestnuts Roasting on an Open Fire, and Siboney, reinforce the audience's sense of deja vu (or should it be deja entendu?).

At the core of the film is Tony Leung's memories. He is trapped by his memories of Maggie Cheung, both having suppressed their love for each other in the past. It now leads him back to room 2046 where they first met.

While in "In the Mood for Love," Tony and Maggie never actually fulfil their love, in 2046, Tony beds a whole string of women. And yet he is not fulfilled. His new loves are hollow, and he is haunted by his memory of Maggie.

Tony has a brief affair with a gambler in Singapore, played by Gong Li. He is attracted to her and asks her to go to Hong Kong with him. She uses a card trick to reject his offer. He leaves in sorrow, but it is Gong Li who sheds tears of regret. Much later on, when Zhang Ziyi has fallen in love with Tony, she asks him not to have any other mistresses, and to be with her only, he rejects her. She sheds tears of sorrow. His act is reminiscent of Clark Gable in "Gone with the Wind" and makes him a cad.