Aaron Boone, a troubled young man plagued by disturbing dreams of a mythical city inhabited by monsters, is led to believe by his psychiatrist, Dr. Decker, that he may be responsible for a string of brutal murders. Decker, whose own dark secrets cast a shadow over his intentions, manipulates Boone's vulnerability, leading Boone to search for Midian, the fantastic city from his dreams. Feeling a deep connection to the place and convinced that he will find sanctuary there, Boone sets out to uncover this hidden civilization.

Boone's quest leads him to a remote cemetery in the Canadian countryside, where he discovers Midian beneath the ground. This sanctuary of monstrous creatures called the Nightbreed offers refuge to those who are different and have been rejected by society. Regarded as outcasts and abominations by the human world, the Nightbreed have created a haven where diversity and monstrosity are accepted and celebrated. Boone encounters a variety of beings within Midian, each with their own unique abilities and stories. Through his interactions, he learns more about Nightbreed society and begins to find his place among them. However, the safety of Midian and its denizens is threatened by the outside world, which fears and misunderstands the Nightbreed, leading to a confrontation between humans and the creatures of the night.