The Enterprise comes to the assistance the USS Yosemite, a science vessel where several crewmen have gone missing after a transporter accident. The Enterprise is unable to transport directly to the ship due to interference, but Lt. Reginald Barclay suggests linking the transporter systems of both ships, allowing them to transport one-by-one to the Yosemite albeit after a lengthy dematerialization/materialization process. Barclay, assigned as part of the team, hesitates on his turn and instead walks away.
Barclay discusses the matter with Counselor Deanna Troi, who teaches him Betazoid mediation techniques to help calm himself. Transporter Chief Chief O'Brien also provides Barclay with some advice on dealing with his fears, speaking how he overcame his fear of spiders, before attempting to transport him over again. Barclay is safely transported to the Yosemite and continues to help the other engineering crew investigate the disappearance. On his return trip, Barclay believes he sees wormlike-creatures in the matter stream that attempt to approach him and touch his arm, but he materializes on the Enterprise without harm. He decides that he is suffering from transporter psychosis, a rare affliction. His paranoia forces Troi to declare him unfit for duty. Barclay asks O'Brien to review the transporter logs, and O'Brien agrees there was a strange surge during Barclay's transport. Barclay asks O'Brien to transport him again, recreating the surge, and Barclay again sees the creatures in the matter stream.
Barclay meets with the senior staff and explains his observations. Captain Picard orders a thorough review of the transport systems and those that have used it recently. Barclay's arm is found to be out-of-phase, and further examination reveals microbes that were not detected by the biofilter. To remove the microbes, Barclay is put through the transport again, holding him in the matter stream for a longer duration to allow the biofilters to work. While in the stream, Barclay sees one of the creatures approach him, and at the last moment, he reaches out to grab it to his body. When he materializes, one of the missing Yosemite crew safely materializes alongside him. Barclay quickly explains that the other crew members are the remaining worm creatures in the matter stream based on their equivalent numbers, and soon they rescue the remaining crew. The Enterprise crew determine that an explosion near the Yosemite during the transport caused the people to become trapped. Later, Barclay and O'Brien meet at Ten-Forward to discuss the nature of fear, upon which O'Brien shows Barclay his pet spider Christina to share with a visible fightened Barclay.