Several of the Enterprise crew members are having difficulty sleeping or have lost track of time, and find themselves having strange emotional responses to normal objects. The affected crew realize they have had common experiences, and with Counselor Troi's help, use the holodeck to collectively reconstruct and refine their fragmented memories and impressions of the events. Their collaboration results in a device like an operating table in a dark room filled with mysterious noises. They come to the conclusion that they have all been to a similar place.
Dr. Crusher examines them, finding evidence of sedation as well as subtle changes to their bodies, such as a microscopic misalignment of the bones in Commander Riker's arm, indicating it has been severed and then reattached. They realize they are being abducted from the ship to be experimented on. When they wonder if this is happening to other crew members as well, they ask the ship's computer to list any missing members and find that two other crew members are currently missing. One soon reappears in his cabin, but dies shortly after he is found, his blood having been transformed into a liquid polymer.
Geordi and Data also discover particle emissions in one of the cargo bays, creating an expanding subspace rift which threatens to breach the hull. They devise a method to counter the emissions and close the rift, but they need a way to trace the emissions to the source. Commander Riker volunteers, as he has been taken several nights in a row. Dr. Crusher injects him with a stimulant intended to counteract the sedative his captors are using, and he carries a tracking device which can be detected from the Enterprise when he is taken. Riker is again taken that night and finds himself in a strange environment on an operating table, near the other missing crew member, surrounded by busy aliens.
Meanwhile, the rift continues to expand, and Captain Picard orders Geordi to begin the attempt to close it. Riker pretends to be unconscious until the aliens are distracted by the now fluctuating rift. He frees himself, picks up the other crew member, and jumps through the rift which is now large enough for them to pass through. They appear in the cargo bay moments before the rift is forced closed. The aliens manage to send a brief energy pulse through at the last second, which disappears through the Enterprise hull and into space. Picard wonders if the pulse is a probe sent by the aliens attempting to communicate with the Enterprise, but Riker, noting their methods which resulted in the death of one of the crew, suspects their motives are less benign.