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The survivors blamed Uchiha Madera. After all, he had single-handedly announced the Fourth Great Ninja War, and if it hadn't been for that, the Mizukage would never have felt the pressure to step up the R&D program.
Originally, it had seemed a brilliant idea. The breeding programs that formed the backbone of the arms race between villages was effective, but excruciatingly slow. Transplantation, while currently in vogue, was inflexible, crude, and so one hundred years ago. Instead, gene therapy seemed the way of the future.
In theory, the idea was simple: splice the desired genes into a viral vector, infect the human carrier, and let the virus insert the desired genes into the genome. In practice, there were surprisingly few complications initially. The genes giving the ability to sense chakra from a distance had been previously sequenced, the biowarfare lab two floors below was willing to modify an adenovirus to contain the desired genes and an integrase, and the intelligence service had plenty of already processed foreign ninja it wanted to get rid of.
Unfortunately, the regular technician from the biowarfare lab was on maternity leave, and the flighty intern taking her place mixed up his vials and instead of using the standard transfection agent, used the experimental virus that had been modified to be highly contagious and wipe out higher brain functioning in its victims. Oops. Lucky for him, he was never reprimanded for his mistake. Unluckily, it was because he, and practically all the researchers in that building died during the initial outbreak.
The outbreak spread, as the common cold is wont to spread, and within a month, the village hidden in the clouds was empty except for the occasional coughing and sneezing biped, mindlessly searching for food, water, and most importantly, chakra.
For the most part, the horde had abandoned Cloud, swarming towards the surrounding communities, since a highly developed chakra system was one of the things that separated humans from the lower beasts (along with language, intelligence, and the opposable thumb.)
For the first few days, the farmers were amused by the former ninja, since the creatures (no longer human?) did nothing more aggressive than crowd and occasionally try to hug them (though the smell of those unwashed creatures was rather offensive), but when the incubation period drew to a close, and one by one, the farmers gained that empty expression on their faces, people started panicking.
The horde spread and spread, towards civilian settlements, where the concentration of people was high enough to attract the creatures, towards groups of ninja, who for once were finding the chakra they unconsciously but constantly exuded was a liability, and to the hidden ninja villages, which shone like beacons in the night sky. Borders closed, trade was suspended, and xenophobia reigned, but nothing could stop the advance. When the gates of a hidden village were closed, and burning oil and exploding tags dropped over the walls to kill the dimwitted creatures, more and more simply continued to swarm, until the bodies were piled as high as the walls, and they scrambled over the corpses of their compatriots and into the village itself.
The village hidden in the leaves had several key advantages over the other villages. Early warning from the teams sent out on missions, the finest medical program in the elemental countries, and the Hyuga clan. They scattered.
They left in groups of no more than two dozen, the ninja painstakingly and painfully leading out the civilians, the elderly, and the infirm at a crawling pace, accompanied by members of the Hyuga clan, who obligingly blocked the tenketsu of the ninjas to hide them from the groups of zombies roaming the country. The groups spread out into the wilderness of Fire Country, with the exception of one team, sent to the heart of Lightning Country.
That team was lead by Shizune, and contained the top medics and researchers of Konoha, along with Tenten, Lee, Neji, and Hinata. The trip to Kumo was surprisingly boring, aside from Sakura and the other medics arguing furiously about the merits of chicken eggs verses cell culture or of killed verses attenuated viruses. Aside from the academics, the only person that enjoyed the trip was Tenten, who rejoiced at finally facing enemies who actually died when a kunai sliced open their throat. Neji mostly moped since he couldn't risk going near the attackers, and unlike Tenten and Lee, was useless without his chakra.
At Kumo, while the mad scientists holed themselves up in the laboratories, Tenten and Lee patrolled the streets and Neji and Hinata raided Kumo for secrets. It was compensation thirteen years overdue, so they made the most of it. In the months they were there, Kumo was filled with maniacal laughter and giggling from the researchers and their four escorts.
Eventually, all good times must end, and the ninja were sent out bearing the vaccine for whoever was still alive. They vaccinated Fire Country and the rest of the world, and extorted enough in the process to take over the world if they wanted to.
In the end, the history books said that Fire Country won the Fourth Great Ninja War, even though it was technically Lightning Country that finished off Madera, who was last seen drooling somewhere in the mountains.