Captain Janeway and Neelix are returning to Voyager from a trade mission with an unusual race called the "Tak Tak", but find the ship adrift with no evidence of an attack, the crew apparently missing, as well as strange bio-electric sensor readings. They board the ship to find it deserted and try to investigate what happened.
While en route to the bridge, the turbolift they are in is attacked and Neelix is sprayed with a mucilaginous liquid. They escape into a Jefferies tube but he quickly begins to get faint and becomes too weak to continue. As Janeway goes to get medical supplies, he is abducted by an unknown life form. Janeway makes her way to the bridge to send a distress message and search for the crew. While doing so, she is bitten by a small flying life form roughly the size of a fly.
She discovers that the crew are in the mess hall, but gets there to find them barely conscious with strange growths on their necks from which life forms are emerging. She is then attacked by a much bigger life form and kills it with a phaser. She makes her way to sick bay and finds the Doctor who tells her that while she was on her away mission, they came across a Garan mining colony where the workers were suffering from a severe viral infection. The Doctor was transported down since, as a hologram, he couldn't be infected. The Doctor determined that the virus reproduces and grows into much larger macroviruses. When he is transported back, some of the virus is transported with him and makes their way from the transporter pattern buffer into other ship systems, subsequently infecting a bio-neural gel pack before the buffer could be purged; the infected gel pack then malfunctions, infecting B'Elanna Torres when she inspects it. The Doctor takes a sample of the macrovirus and succeeds in making a cure; however, the macrovirus had already multiplied and grown large enough to break out of the quarantined area and infect the rest of the ship. At that point, they had grown large enough to pose a significant threat to anything emitting a bio-electric field, thus keeping the Doctor from leaving sickbay to treat the crew as any attempts made resulted in attacks that would have destroyed his mobile emitter.
The Doctor treats Janeway with the antiviral while she devises a plan to vent it to the crew via the ship's environmental systems. At that point, however, the sick bay doors suddenly come under attack by the macroviruses, and both she and the Doctor make their way to the Jefferies tubes.
On their way, they split up in order to improve their chances of getting to the environmental controls, but the Doctor is overwhelmed by the macroviruses and takes refuge in a shuttle. Janeway reaches the environmental controls, but Voyager is then attacked by the Tak Tak who on receiving the distress call, are 'purifying' the virus by the only means they know - destroying the viral threat by destroying the ship. Janeway explains to the Tak Tak that they have a cure and they agree to temporarily withdraw their attack. But the damage to the ship means that the original plan would no longer work. Janeway rigs up an "Antigen bomb" that will distribute the antiviral, and lures the macroviruses into a holodeck with holographic characters as bait. The macroviruses attack the holographic characters but before Janeway can throw the bomb into the holodeck, she is attacked by a macrovirus. She manages to kill it, and throws the bomb in just in time, wiping out the macroviruses. The Tak Tak are grateful upon being informed and receiving the cure. The Voyager crew is finally cured.