While Chi is on her way to work, she notices the third part of the book series "A City With No People" on the shelf of a bookstore. While she flips through the pages, she is grabbed from behind and is kidnapped. Hideki comes home from prep school and returns to find Chi missing.

Chi is still missing, and Hideki is enlisting as much help as he can to find her. A strange e-mail image gets sent to him and Shinbo from an untraceable email address. It turns out that this is a map for the house of Chi's abductor, Dragonfly, and he is carrying out research to find out what Chi is.

Hideki and Chi help Shinbo move out of the apartment to live with Ms. Shimizu (who is now married to him). Then they arrive at Minoru's house, where he is trying to find information on Chobits. Minoru, who has not been sleeping enough, passes out, and Yuzuki (Minoru's custom-made Persocom) decides to try to hack the Chobits database herself.

Ms. Hibiya secretly leaves Chi the fourth book in the "A City With No People" series. Hideki meets with Shinbo and shares his feelings for Chi. Ms. Hibiya reveals to Hideki that her husband was the one to create Chi and the other mysterious girl, Freya. She tells Hideki that Chi used to be called Elda and, like her sister, was created to be loved and fall in love with others. Chi then tells Hideki that she loves him.