After a fitful night's sleep, the crew realizes they all had nightmares involving the same alien. They become concerned when several crewmembers cannot be awakened. Hoping to find out more about the alien, Chakotay attempts a technique called lucid dreaming, which will allow him to control the events of his dream. If he needs to awaken, he can tap his hand three times.

After falling asleep, Chakotay encounters the alien and demands to know what's happening to the crew. The alien explains that for his species, the dream state is their reality. For centuries they've been harmed by "waking species," and now they are retaliating. He tells Chakotay that if Voyager leaves their space, the crew will awaken. Chakotay comes out of the dream and orders a course for the alien border. But once there, a ship begins firing at Voyager. It's the dream aliens.

The aliens beam aboard, taking the ship. As the crew looks for ways to regain control, Chakotay sees a visual cue that lets him know he's still dreaming. After tapping his hand, Chakotay wakes up in Sickbay, this time for real. The Doctor informs him that the entire crew is asleep, and their brain patterns show they are all experiencing the same dream. Chakotay realizes that they're involved in a communal dream. The aliens have the advantage in dreams, but if Chakotay can locate the sleeping aliens while he's awake, he'll have the upper hand. In the dream, Janeway and the others are being held hostage but they begin to suspect that they are dreaming. When the Captain is unharmed by a warp core explosion, they know it's true.

The closer Chakotay gets to the sleeping aliens, the harder it is to stay awake. At last he finds them in a cavern, clustered around a large transmitter that is responsible for maintaining the dream state. He uses a stimulant the Doctor gave him to wake one of the aliens and commands it to deactivate the device. Before Chakotay falls asleep and enters the communal dream, he tells the Doctor to deploy a torpedo at the cavern if he doesn't hear from him in five minutes. Under threat of total destruction, the alien leader is forced to neutralize the transmitter, and the crew awakens, freed from alien control.