The Plague of New Germania was a virus developed by the Styx. It killed all mammals, including humans and Styx. The virus was stolen from The Laboratories by Drake before they were destroyed. Drake's immunologist friend Charlie weaponized it, making it transmittable by air in addition to direct contact. It was only used once, accidentally, in the Garden of the Second Sun, where it caused an ecological catastrophe and wiped out the civilization of New Germania and the "Bushmen."
"It's deadly with a capital D."
This infectious agent was a virus. Like all viruses, the plague was made of a protein coat surrounding its genetic material, and receptor proteins to latch onto its host cell. It used its host cell to reproduce itself, killing the host cell in the process. The host cell was evidently something all mammalian species had in common, as they were all susceptible to it, and the Styx had apparently accquired that cell during one of their Phases. The virus was first only spread only in water, but it was altered by Charlie to also be airborne in its transmission. After a host contracted the virus, it would die in less than twelve hours. The symptoms of the virus included lesions on the host's skin, fever, coughing up blood, insanity, and eventually death.
"It's just us, and the birds and the fish left."
"Academics do like to boast to each other."
The virus was one of many that were carried by the plague snails of the Eternal City. At some point, the Scientists extracted it from a plague snail and tried it on a range of suspects, including humans and Styx, and the results awed them. It killed all mammals.
"I had the opportunity to grab it from the secure vault in the secondary path lab."
Before his escape, the captive Topsoiler who called himself "Drake" overheard several scientists talking about the virus. Several years later, he had the opportunity to steal it when he returned to the Colony to destroy the Laboratories. While his companion Chester Rawls searched upstairs for captive Topsoilers, Drake helped himself to the samples of diseases the Styx had in storage. Ironically, this didn't help him at the time, as this detour slowed him down and he was consequently incapacitated by the Styx turncoat Eddie, although he later escaped.
"And when I was in London, I had my friend Charlie weaponize it..."
Drake gave the pathogens he'd stolen to his friend Charlie, who enhanced the plague to help it spread and also developed vaccines against all of the diseases. Drake then gave the vaccines to every member of his group.
Drake took it down to the inner world, not intending to actually use it, but keep it as a deterrent against the Styx in case something went awry in his plan to seal the inner world with nuclear bombs. He revealed its existence to his compatriots in the Colony. When he reached the inner world, his plans did go awry. As his group prepared to exit the Garden of the Second Sun, they were ambushed by a Styx patrol led by Rebecca One and Vane. When it was apparent that the Styx girl was about to kill Will, he took the bullet meant for Will, and swept Rebecca One into the void before she could fire another. As they fell, he detonated the nukes, sealing the inner world. The EMP generated by the blasts killed Sparks, whom Drake had given the virus to, by overloading the circuitry in his head. As Sweeney's body hit the ground, the test tube holding the virus shattered, releasing the virus into the atmosphere. The virus then quickly killed every man, mammal, and Styx in the inner world, except for Will and Elliott, who'd been vaccinated for it.
"Not just humans, but Styx and many of the more developed lifeforms are susceptible to it."