For several years in the year 2059, the planet has been tormented by aliens. Dr. Noguchi and his assistants Maki Agata and Takuto Kaneshiro attempt to revive the professor's experiment, a giant Bio-Mechanical alien dubbed Frank, in order to discover more about these aliens. The alien 'comes to life' during this procedure, and the lab is destroyed, leaving Takuto as the lone survivor and the alien vanishing into the countryside. Frank meets Hattie, an emotionally disturbed young girl whose parents were slain in the first "close encounter" conflict, while roaming the countryside. Despite the fact that she is able to converse with Frank, they are quickly apprehended by a secret agency known simply as 'Funeral.' Takuto, on the other hand, wakes up in a strange place.