The protagonist is Parton, a posh upper-class man who volunteers for an adventure mission. After being blown apart by a rocket launcher, only his head survives. He is rescued and given a robotic body made from scrap parts, with his head attached on top, which is why the film is named Junk Head.

Parton's mission is to study the denizens of the lower levels, who were originally cloned from humans to develop the underworld. He is tasked with researching the secrets of their reproductivity in a dystopian underground world.

Parton encounters a unique society formed by artificially created intelligent species who rebelled against humanity 1,600 years ago. The underground is a dystopia filled with dangerous monsters and bizarre characters, including a scientist and his three henchmen who resemble demented, cyberpunk versions of the penguins from Madagascar and behave like the Three Stooges.

Parton suffers amnesia due to the trauma from his head being blown apart and reattached to a robotic body. As his memories slowly return, he resumes his initial quest, which drives the episodic middle part of the movie filled with misadventures in the underworld.

The underground world is set in a far future where humans have gained immortality but lost fertility. The film is the first part of a trilogy, with the sequel Junk World (2025) set 1,042 years before Junk Head, featuring the same central robot character known as Robin. The sequel explores the origins of the underground society and the Mulligans, artificial life forms that rebelled against humans.