A giant virus takes over the ship.
Returning from a trade mission with the Tak Tak, Janeway and Neelix find Voyager adrift and its crew missing. Insect-like creatures fill the ship, attack Neelix and bite Janeway, and she finds the crew unconscious with growths on their necks. In sickbay the Doctor explains that, after treating a sick mining colony, he unknowingly brought back a macrovirus, a germ that can grow to a visible size and reproduce in the crew and the ship's bioneural gel packs.
The Doctor has made an antiviral but cannot spread it while the creatures hunt anything with a bioelectric field. Janeway fights through the ship as the Tak Tak, fearing contagion, prepare to destroy it. She lures the virus to a holodeck full of simulated people, seals it in and floods it with the cure. The third-season episode is an action story built around Janeway, who carries most of it alone.