Susumu Nakoshi is a middle-aged man who spends his days between a lavish first-class hotel and a park full of homeless people. One day, an eccentric young man approaches Nakoshi in search of subjects willing to partake in trepanation—the procedure of drilling a hole in the skull.

This mysterious person claims that Nakoshi is the perfect man for the experiment. Initially rejecting the offer, he doubles back on his decision after his car gets towed off. Nakoshi agrees to let Manabu Ito, a 22-year-old medical student, drill a hole in his skull in exchange for 700,000 yen. The procedure bears no results at first, with Nakoshi showing no abnormalities. This normalcy comes to an abrupt end, however, when Nakoshi begins seeing the homunculus in every person. With his perception distorted, how will Nakoshi face these homunculi?

Homunculus was published in English by Seven Seas Entertainment as 2-in-1 omnibus volumes from June 27, 2023 to July 2, 2024. It was also published in Brazilian Portuguese by Panini Comics from April 2008 to April 2014; and in Italy from December 17, 2020, to September 16, 2021. In addition, the first nine volumes were released in Spain by Ponent Mon from September 2005 to October 2008.