The troubled young man, Aaron Boone, is plagued by recurring nightmares about a place called Midian, where supernatural beings are said to reside. In an attempt to find answers and escape his troubled life, he seeks out a psychiatrist named Decker. However, Decker is not the helpful professional he first appears, and instead convinces Boone that he is a serial killer responsible for the murders that have been happening in the area.
Boone seeks refuge in Midian, a hidden world of monsters and mutants located beneath a cemetery. The beings of Midian are friendly and accepting of Boone, seeing him as one of their own. However, the monsters' secrecy is threatened by the outside world, as Decker leads a group of vigilantes to destroy them.
As the battle between the humans and monsters escalates, Boone discovers his true identity as a Nightbreed, a member of the supernatural community, and becomes determined to protect Midian from destruction. In the end, the two sides clash in a violent battle, with Boone leading the Nightbreed in a fight for their existence.
Ultimately, Boone sacrifices himself to stop the violence and save Midian, while the survivors flee into the night, seeking a new home away from human persecution. Nightbreed showcases the theme of acceptance and prejudice, demonstrating that not all monsters are evil, and that sometimes the true evil lies within humanity.