Returning from a trade mission with the Tak Tak, Janeway and Neelix are perplexed to find Voyager adrift in space. After landing their craft in the Shuttlebay, the pair notes there are no crewmembers in sight and that many of the ship's systems are off-line. While investigating the seemingly empty ship, their turbolift is halted by several lifeforms, one of which pokes a hole in the door with a large stinger. The stinger sprays Neelix with slime, but the pair is able to escape. Not long after, Neelix falls ill and Janeway goes to find an emergency kit. When she returns, he's gone.
Now on her own, Janeway arms herself with weapons and goes to the Bridge, where she is stung by one of the bizarre lifeforms. In the Mess Hall, she discovers unresponsive, ailing crewmembers and a giant flying creature, which tries to attack Janeway.
Fleeing to Sickbay, Janeway finds the Doctor holed up with a phaser. He reports that the ship is infected by a strange alien macrovirus. He explains that while Janeway and Neelix were away from the ship, Voyager responded to a medical distress call from a mining colony stricken by a virus. A few of the "bugs" migrated back to the ship when the Doctor returned, and since then, they've spread throughout the ship's systems, and ultimately to the crew. The Doctor has come up with an antigen but he hasn't had the chance to test it, since the huge, mature versions of the virus — such as the one that came after Janeway — have prevented him from leaving Sickbay. Now infected herself, Janeway volunteers to test the antigen and is cured. But there's still the problem of distributing the antigen to the ailing crew.
Janeway comes up with the idea of distributing the cure in gaseous form through the ship's environmental system. Using her arsenal, she blasts her way through the ship until she reaches the controls. But before she can disperse the antigen, Voyager is fired upon by the Tak Tak, who want to exterminate the virus by destroying the ship. Janeway tells them about the cure and asks them to stop shooting long enough for her to treat the crew. They give her an hour. Unfortunately, the environmental controls have been damaged, but Janeway figures out how to put together an antigen bomb, which destroys the virulent invaders.