The plot generally focuses on the custody battle for Ryunosuke and the attempts by Akiko and Mishima Heavy Industries to reclaim Nuku Nuku's body, which often involves amusingly larger-than-life battles between Nuku Nuku and military hardware produced by Mishima Heavy Industries.

Two episodes also deal with a one-sided war between Nuku Nuku and another android named Eimi, who suffers from an over-the-top inferiority complex and envies Nuku Nuku's more stable design. As it stands, Eimi was made after her and seeks to transfer her programming into Nuku Nuku to ditch her own body, which Akiko calls "a piece of junk." In spite of Eimi being more emotionally unstable than Nuku Nuku, both their fights end in a draw.