After Tuvok recovers, he reveals that they were attacked by an unidentified ship that emerged from a dark matter nebula. Janeway orders Voyager to head back to the nebula to investigate, but before they reach it, the ship changes course. The navigational computer implicates Paris, but he denies having made the change. A short time later, Torres initiates a warp core shutdown, but like Paris, she can't remember instigating the actions. When the Doctor examines the pair, he discovers that a strange brainwave pattern was superimposed on them during the tampering incidents — which could mean that an alien entity momentarily seized control of their minds. As a precaution, Janeway transfers the ship's command codes to a non-organic source: the Doctor.

When Kes tells Janeway that she has been "sensing" an alien presence on the ship, Tuvok suggests that he perform a mind-meld with the Ocampan to help her focus her telepathic abilities. But a short time later, the two are found unconscious, the result of an energy discharge similar to the one that hit the shuttle, according to Tuvok. A short time later, someone disables the Doctor's program. With him out of the picture, the command codes revert to Janeway, who decides to divide them between herself and Tuvok. The unseen force tries to take over Janeway, but the crew incapacitates her. It jumps to Kim, and then Lieutenant Durst, before Tuvok finally stuns everyone on the bridge.

A series of clues turns up in quick succession, all of which imply that Tuvok has been lying to the crew. There was no ship in the nebula, and Kes' injury now appears to have been the result of a Vulcan nerve pinch. Under increasing suspicion, Tuvok takes over command of the ship and orders it into the nebula, where he says the Komar — others of his kind — await. But before they can get there, something makes Torres eject the ship's warp core. Since they now know that Tuvok, under the control of the Komar, has been trying to bring them all to the nebula all along, who has been acting against him, trying to keep Voyager out? All signs seem to indicate that it is Chakotay.

Realizing that the Komar want to extract their collective neural energy, the crew manages to overpower the Vulcan at last. The lifeform leaves his body to join the others of its kind in the nebula. Voyager's crew needs to leave the area, but since the possessed Tuvok plotted the course in, they are uncertain how to get out of the nebula.

Down in Sickbay, Neelix is suddenly compelled to rearrange the markers on Chakotay's medicine wheel. Janeway realizes that it is a message from her first officer, a map showing them the correct course. They escape from the nebula just in time. Later, the Doctor finds a way to reintegrate Chakotay's displaced neural energy with his body and he revives at last, pleased that he was able to help protect the crew, despite his disembodied condition.