The Voyager crew recovers its shuttlecraft containing Commander Chakotay and Chief of Security Tuvok after they had left to explore a nearby dark matter nebula. Tuvok is unconscious, but Chakotay appears to be brain dead, lacking any neural activity. The shuttlecraft shows evidence of energy weapon attacks. Mourning their loss, Captain Kathryn Janeway orders Voyager towards the nebula to learn whom the attackers were. B'Elanna Torres, a close friend of Chakotay, uses a Healing Wheel, one of Chakotay's spiritual talisman, to hope to guide Chakotay's spirit to his body.
En route to the nebula, the ship suddenly changes course away from it, though Lieutenant Tom Paris, at the helm, denies doing so. When it happens a second time, it is confirmed to be due to Paris' actions, despite him not being aware of doing so, and he is relieved of duty to determine if he is being possessed. As the crew follows a trace of an engine pattern used to avoid navigational obstacles in the nebula, the ship's engines are suddenly deactivated, apparently by Torres who also has no recollection of doing so. The Doctor discovers a common memory pattern between Paris and Torres at the times they acted possessed. The crew believes there is an entity aboard that can possess the crew temporarily; Kes states that she has felt such a presence, and Tuvok offers to perform a mind meld to try to help her identify it. However, the two are soon found unconscious, Kes herself in a coma. Unsure of the intentions of the entity, Janeway orders the command codes to the Doctor, who cannot be possessed; however, shortly afterwards, they find the Doctor's program deactivated. At the suggestion of Tuvok, Janeway decides to divide all command codes to be entered by herself and Tuvok, believing the entity can only possess one of them at a time.
Torres and Paris discover evidence that points to Tuvok being responsible for several of the events. When these come to light, Tuvok reveals that he is a noncorporeal alien known as the Komar, seeking to bring Voyager's crew to the center of the nebula so that his people can feed on their neural energy; he takes the command crew hostage as he brings the ship about. Suddenly, the warp drive is ejected from the ship, halting their progress. Janeway realizes there is a second entity aboard Voyager and Torres confirms that it appears to be Chakotay. The crew overpower the possessed Tuvok, and force the Komar entity away from the ship with a magneton scan.
Though the hostile entity is gone, the ship is deep within the nebula without a safe means to escape. Chakotay, through Neelix, uses the Healing Wheel to show a series of planetoids to be used as guidance to escape the nebula. The crew follows this, and safely leave the nebula after recovering their warp core. Once the Doctor is back on-line, he is able to help restore Chakotay's mind to his body, and recover Kes from her coma.