Stardate 50425.1: Returning from a trade mission with the Tak Tak, Janeway and Neelix attempt in vain to contact Voyager. When they find the ship and land the shuttle, there is no sign of the crew, main power is offline and a bioelectrical field blocks the sensors. Alien lifeforms have taken control of the ship, and Neelix is incapacitated and dragged away by one of them. Janeway finds some of the crew unconscious in the mess hall. In sickbay, the Doctor tells her that the alien intruder is the macroscopic form of a virus that he unknowingly brought aboard after he tried to cure a virus outbreak on a Garan mining colony. The Doctor has synthesized an antigen, and in order to distribute it Janeway proceeds to the environmental control station. But an attack by the Tak Tak, who want to "purify" the ship, disables the environmental control system. Janeway decides to lure the viruses into the holodeck by creating holographic characters with infrared emissions as possible victims, and she releases an "antigen bomb" that eventually destroys the viruses.

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