After Seven of Nine returns from an away mission she finds the crew have discovered what they think is a wormhole leading directly to Earth. Suspicious of everyone's unfettered optimism despite signs the anomaly may not be all it appears to be, Seven accesses Captain Janeway's logs. At first, the captain grimly reports that secondary scans determined that the wormhole was a deception, but in supplemental logs, Janeway suddenly believes it is real and that there is nothing to worry about.
Seven locates an alien vessel in the wormhole after a re-scan; not originally detected by Voyager's sensors, she hails it. The alien, Qatai, warns her not to go into the anomaly, and that Voyager is being deceived, but they are cut off when Janeway routes power from the lab to another system. When Naomi Wildman tells Seven that she thinks everyone is acting strangely, Seven realizes they are the only two unaffected by whatever is manipulating the crew, Seven because she cannot remember Earth, and Naomi because she has never been to Earth and considers Voyager her real home. She also finds that The Doctor is not affected either, since he is a hologram. The crew is suddenly and conveniently ordered by Starfleet to take the Doctor offline to avoid system interference from the wormhole, and to put Seven in stasis to avoid attracting Borg attention while Voyager passes through the wormhole.
Seven knows that something is manipulating the crew, and compelling them to enter the wormhole with the promise that they will see Earth, but no one will listen. She decides to act. As Chakotay escorts Seven to her alcove, she tricks him and erects a forcefield to contain him. With Naomi keeping security at bay, Seven transports to Engineering and stuns B'Elanna with a phaser. After erecting another forcefield there, Seven attempts to shut down the impulse drive to keep Voyager from entering the wormhole. Janeway transmits a electromagnetic surge to the engineering console that knocks Seven out.
With Seven incapacitated, Voyager proceeds to enter the wormhole. Once they enter the anomaly, the crew falls unconscious and begin to hallucinate. When Naomi wakes Seven, the two look outside Voyager's windows and see that they are not inside a wormhole, but some kind of organic chamber. Seven hails Qatai and convinces him to beam aboard. He explains that the crew has been a victim of telepathy and psychogenic manipulation from a bioplasmic organism, a beast that consumes starships by telepathically preying on their crews' desires. The creature also has the ability to change sensor readings, which explains why Voyager's sensors did not fully detect the deception. Qatai has been trying for years to destroy the creature, which killed his family, not always successful at evading its deceptions, as he at first believes Voyager and her crew to be hallucinations.
After reactivating the Doctor's program, Seven informs him that Voyager is being devoured in the digestive chamber of the organism. Realizing that bodies are designed to expel foreign objects, they plan to fire one of Qatai's tetryon-based weapons at a pocket of antimatter released from Voyager's warp core, which would make the creature literally vomit Voyager and Qatai out. After firing the first weapon, Seven believes that Voyager has been expelled from the organism. But Qatai hails her from his ship and warns her that now she is the one being deceived, because getting out of the organism is what she really wanted, and the creature simply made her think that one weapon burst would do the trick. The Doctor confirms this with his own scans, and Seven takes Qatai's advice and releases more antimatter. It creates another, larger reaction in the beast that causes it to finally expel the two ships through its esophagus. After having the Doctor make sure that they really are out of the creature, Qatai departs and Janeway and the others regain consciousness, Voyager resumes its course to the Alpha Quadrant, but Qatai returns to the beast, determined to defeat it.