The crew is stuck in nightmares.
The senior officers all have nightmares, and in each one the same unknown alien appears. Harry Kim and other crew members cannot be woken from deep sleep, and the Doctor tells everyone to stay awake. Chakotay, who has practised the lucid dreaming of his people, uses it to meet the alien, who explains that his species live in a dream state and see Voyager as a threat.
Chakotay seems to wake, but finds himself in another dream as the aliens take over the ship. When he truly wakes, he locates the aliens' sleeping bodies in a cave on a nearby planet and threatens to destroy them with a torpedo. He falls asleep from exhaustion and delivers his warning inside the dream, and the aliens agree to release the crew. The fourth-season episode is a showcase for Chakotay's heritage, and it plays with dreams nested inside dreams, ending with the crew left only with insomnia.