It does seem to be rather rushed at the end and the author seems to have given up on some of the other stuff that was it building up to, but got ignored or left out in order to finish the series. I guess this leaves the reader to somewhat of an open ending, as in leaving the reader to imagine what happened during the 3 years and after this chapter. It's still not over as it's still world wide (as seen in the extras).
@bthao the answers were in the extras (vol.1-9) not available on this site.
There were some incidents concerning September 1968, the marketplace area of Nazake Marsh (now known as Kuchina River), Dando City (now known as Megurigaoka since 1979) of a natural bacteria (native to Megurigaoka) of an unknown cause (not war or terrorism). The Megurigaoka School Song mentions: "In the Kuchina River is the poison breath of the great nine-headed serpent" but that would be silly? Looks like some bacteria in the river that people ended up getting through playing around in the water and eating the fish.
When it was discovered, the government sent out leaflets and stuff to inform people and managed to contain the area, however, there were a lot of cover-ups and there was a cleansing by fire and quarantine. They made it a secret (since a lot people died and very few talked about it no one really knew about what really happened and become a folktale: "First among the seven hills is the saint whose blade glitters like heaven. Roiling in the Kuchina River is the poison breath of the great nine-headed serpent. Seven days and seven nights of fighting. What fell from heaven was tears of blood soaked deep into the ground. The remains of the fires were a real horror" and the fact that was around the time of other wars (the exploded bomb) and the events of the Itai-itai disease [1])
They provided private information booklets and to prepare for if it ever happened again. (Everything is explained in the evacuation manuals, school book, world map, radio frequency notes and newspaper articles). So we get Randell Corp., it seems a private government organisation decided to use this bacteria for cures and biological weapons. Unfortunately, present day September 2008 someone was careless, didn't clean themselves after leaving work and it spread. A simple accident by an unreliable person. Rather than owning up to their errors they become split over it one side trying to help wanting to survive the other killing everyone, depressed and believing it's the end of humanity.
The water filtration was suppose to cleanse the water, but looks like it was ineffective to the bacteria but as the bacteria was weakened and the people who drank it over the years helped their immune systems. This is most likely unexpected and another accident. If had the water filtration worked properly as it was suppose to then there wouldn't have been a potential cure.
[1] 1968: Itai-itai disease is formally recognised as a public hazard disease. Itai-itai disease saw mass cadmium poisoning in the rivers of the Toyama Prefecture.
https://en.wikipedia.org/wiki/Itai-itai_disease