It is sometime in the future, where a certain European city extends far underground, even secret, dark levels that have the key to the past. Ex-assassin Mihai has returned and is living with Kiri, who now runs a restaurant. Sword-wielding Naoto, Haine (white hair), a mysterious product of genetic engineering and his sometime partner Badou (eyepatch).

When computers start to look like humans, can love remain the same? Hideki Motosuwa is a young country boy who is studying hard to get into college. Coming from a poor background, he can barely afford the expenses, let alone the newest fad: Persocoms, personal computers that look exactly like human beings. One evening while walking home, he finds an abandoned Persocom. After taking her home and managing to activate her, she seems to be defective, as she can only say one word, "Chii," which eventually becomes her name. Unlike other Persocoms, however, Chii cannot download information onto her hard drive, so Hideki decides to teach her about the world the old-fashioned way, while studying for his college entrance exams at the same time. Along with his friends, Hideki tries to unravel the mystery of Chii, who may be a "Chobit," an urban legend about special units that have real human emotions and thoughts, and love toward their owner. But can romance flourish between a Persocom and a human?

Ryuunosuke Natsume is the son of genius inventor Kyusaku Natsume and overbearing Akiko Natsume, CEO of Mishima Heavy Industries. Using funds from his wife's company and the brain from his son's beloved cat, Kyusaku creates a revolutionary android called Atsuko "Nuku Nuku" Natsume. To Kyusaku's disgust, Akiko wants to use her husband's technology to create weaponized robots for her company's customers, resulting in Ryuunosuke getting caught within the explosive fights between his parents The android Nuku Nuku tries to live as a normal high school student, adopting the role of Ryuunosuke's elder sister, but usually ends up acting as her family's protector. Nuku Nuku will do anything to protect the ones she loves.

Unaired episode 11.5 included with the second Blu-ray/DVD volume.