The story picks up 25 years after the murder of Laura Palmer in the small town of Twin Peaks. Agent Dale Cooper remains trapped in the Black Lodge, an alternate dimension filled with strange and surreal elements. Meanwhile, his doppelgänger, controlled by evil forces, is committing crimes in the real world. Cooper's return to Twin Peaks is triggered by a mysterious series of events across the country. A new investigation begins when traces of his doppelgänger's actions surface, drawing attention from various law enforcement agencies and involving former and new residents of the unsettling town.

The narrative expands beyond Twin Peaks, exploring different locations and characters connected by a supernatural mystery. Gordon Cole and Albert Rosenfield, high-ranking FBI officials, delve deeper into the enigmatic situations surrounding Cooper’s doppelgänger. Elsewhere, in South Dakota, a murder investigation leads to a connection with the small town's bizarre happenings. Mystical elements take center stage as Cooper navigates a mind-bending journey back to reality, involving otherworldly figures and cryptic visions. As the strange occurrences ripple through the fabric of multiple realities, characters face challenges that test their understanding of space, time, and identity. The show weaves numerous subplots, blending horror, mystery, and surrealism, gradually building a tapestry of interconnected stories that leave audiences questioning the boundaries between dreams and reality.