A mysterious Bajoran man, Teero Anaydis, sits in a musty room with Bajoran tapestries and drawings of Maquis vessels, reciting a mysterious chant while staring at a monitor displaying Maquis crewmembers from USS Voyager.
On board Voyager, Tom Paris surprises his new wife B'Elanna Torres by taking her to his new holoprogram — a classic 20th century-style movie theater. In the theater, they discover that Crewman Tabor is sitting at the front completely unconscious. When the Doctor examines Tabor, he concludes that his injuries are the result of an attack, as evidenced by the microfractures on his cranium and contusions along his shoulder. Captain Janeway then appoints Tuvok to investigate the case. Tuvok's initial belief is that a member of the crew is responsible.
Later, crewmen Yosa and Jor are working in engineering when Yosa reports that there is a problem in the system and he goes to investigate. As he crawls through the hatch into a Jefferies tube, the lights suddenly go out. Then, a bright light shines in Yosa's face as someone approaches. Yosa, feeling threatened, crawls through another hatch but is unable to get the computer to seal the hatch shut. Again, the bright light shines on Yosa and he's knocked unconscious. Jor soon discovers him and takes him to Sickbay. The Doctor examines Yosa and concludes that Yosa was attacked, having the same microfractures and contusions as Tabor. Janeway and Chakotay come to realize that all the victims are former Maquis.
Meanwhile, Paris and Kim are conducting an investigation in the holodeck movie theater, trying to capture a negative image that the intruder left behind. Their efforts show two humanoid figures — one is Tabor but the other is unrecognizable. Tuvok requests that they work on increasing the resolution of the images. Later, he tells Kim that for security reasons he reads all crew mail in the last data stream from Starfleet, which includes a letter from Kim's cousin. Tuvok implies that Kim is a suspect, by pointing out that the letter mentions the Maquis killed Kim's friend years ago. As Kim defends his innocence, Tuvok becomes strangely perturbed. Later, Chakotay finds Torres unconscious in a cargo bay, and sees Tuvok heading towards him. To Chakotay's surprise, Tuvok grabs him by the throat and mind melds with him until he loses consciousness. While Chakotay and Torres are treated in Sickbay, the other victims awaken with no memory of what happened to them.
Tuvok continues the investigation sleeplessly, with no memory of having attacked Chakotay. At Janeway's urging, he returns to his quarters to meditate. Suddenly, he has flashbacks of victims in Sickbay, Yosa in the Jefferies Tube and Chakotay in the cargo bay. Then Tuvok enters the bathroom and sees Teero's reflection in the mirror and a bruise he received in his attack on Chakotay. Disturbed, Tuvok rushes to the holodeck where Janeway and Kim are investigating, and learns from the computer that he was in the movie theater during Tabor's attack and that the height and weight of the negative-image figure matches his own description. Tuvok then hears Teero's voice telling him to ignore his doubts — and pulls a phaser. Tuvok resists his own urges, gives up the weapon, and admits to being the attacker, telling Janeway that he should be detained.
When Janeway visits Tuvok in the brig, he explains there is a voice trying to control his mind with Bajoran incantations. Tuvok also says that it was he who attacked Maquis crewmembers and performed mind melds on them, but without knowing why. Tuvok recounts that the attacks started after he received a letter from his son. Janeway, Chakotay, Seven and Paris then view the letter from Tuvok's son and discover that it contains a subliminal message, one of Teero chanting. Chakotay recognizes Teero as a vedek who worked with the Maquis performing mind control experiments, until the Maquis found him too extreme and fired him, earning his enmity.
Janeway meets with Tuvok again in his cell to discuss Teero. Tuvok recalls meeting Teero seven years ago at a Bajoran temple. Teero had uncovered Tuvok's true identity but instead of revealing his background to the Maquis, had subjected Tuvok to torturous mind-control experiments in his laboratory. Janeway urges Tuvok to tell her more, but Teero appears to Tuvok and tells him to complete his mission. Tuvok struggles to stay in control of his mind, but cannot. Instead, Tuvok sends Chakotay a command in the Bajoran language, and his behavior changes. Chakotay goes to Sickbay, fires his phaser at Paris and gives Torres the same Bajoran command. Together they gather the other former Maquis members who were also victims of Tuvok's attacks. They obey Chakotay's commands and fire at the Voyager crewmembers.
Janeway takes the ship to red alert and tries to contact the Bridge, but there is no response. Chakotay finds her and announces that he is in charge. Chakotay tells Janeway that Teero helped them remember that they are Maquis members and that the rebellion on Voyager is not yet over. He releases Tuvok and detains Janeway in the brig. While the Maquis make plans to abandon the Starfleet crew on an M-class planet, Chakotay tests Tuvok's loyalty by commanding him to fire a phaser at Janeway. Tuvok fires the phaser, but nothing happens because the weapon is defective (deliberately so). Then, when Chakotay's back is turned to Tuvok, the Vulcan grabs Chakotay by the neck and performs a mind meld that brings Chakotay back to normal. After that, Chakotay hands control of the ship back to Janeway. Tuvok explained to Janeway that he had a "hunch" that Chakotay would never have given him an operational weapon if he had doubts about his loyalty.
Eventually, the rest of the Voyager crewmembers become normal again, and Tuvok joins Janeway and the others at the movies.