The story is presented through a series of flashbacks, as some of the young adults are questioned at a police station about their time spent in the woods.
The story begins in Burkittsville, Maryland, where the release of the original Blair Witch Project has attracted a group of young tourists. They want to find the Blair Witch, and hire Jeff, who has made a business of leading tours into the Blair Witch's woods called the BlairWitch-Hunt. They venture into the woods to camp for the night.
They wake up the next morning with no real memory of the night before, lack memory of five hours, and videotapes shot during the night seems unclear. Over the course of the rest of the movie, several of the tourists are murdered, and the remaining individuals are suspected as the killers. It is never made clear whether the murders are caused by witchcraft, the still-never-seen Blair Witch, or some other cause. The people left alive claim to have no memory of most of the deaths, and recall instances of possession or suicide, but videotapes taken during the events all show the living tourists killed their friends.