So, this is essentially a Rats of NIMH AU (Alternate Universe); as in canon, a group of rats are captured by scientists working for a laboratory located at the National Institute of Mental Health (NIMH), and the subsequent experiments performed on the rats increase their intelligence to the point of being able to read, write, and operate complicated machines, as well as enhancing their longevity and strength. This increased intelligence and strength allows them to escape from the NIMH laboratories and migrate to their present location. The rats have a literate and mechanized society; they have technology such as elevators, have tapped the electricity grid to provide lighting and heating, and have acquired other human skills, such as storing food for the winter. As such, these rats adopt "The Plan," which is to abandon their lifestyle of dependence on humans, which some rats regard as theft, for a new, independent farming colony. One rat, Jenner, disagrees vehemently with The Plan and leaves the colony with a group of followers.
However, unlike in canon, the experiments which increase the rats' (and mouses') intelligence in this AU are conducted by administering a viral-based drug, derived from Hantavirus. This intelligence-enhancing viral pathogen doesn't make the rats and mice sick (any more than regular Hantavirus does), and simply boosts the intelligence and strength of any infected rodents to the canonical level. However, this pathogen also causes Hantavirus pulmonary syndrome (HPS) for any infected humans, and unlike pre-existing Hantavirus species, the NIMH Rat Virus can also be transmitted through droplet and/or fomite transfer, instead of being limited to transmission via aerosolized rodent excreta, infected blood and body fluids (enabling it to spread in the same manner as Plague and Influenza, rather than in the same manner as Ebola). The NIMH Rat Virus has a comparable fatality rate to Sin Nombre virus, with a fatality rate of around 35%; and just like Sin Nombre Virus, there's no cure.
So, how would you see things playing out next in this AU, in the aftermath of the Rats' break-out from the NIMH laboratory facility, and the establishment of their colony? The NIMH Rat Virus has a far lower fatility rate than the Simian Flu did in Rise of the Planet of the Apes (35%, as opposed to 99%), so far fewer people will die in the ensuing epidemics; but unlike the Apes, who are vastly outnumbered by humans, the total world population of rats and mice already exceeds that of humanity by a huge margin, by at least 4:1 even before the imminent Rat Virus pandemic takes its toll. And as the pandemic spreads outwards, in the aftermath of Nicodemus' and Jonathan Frisby's orchestrated outbreak from the NIMH lab, all of the other mice and rats in the world will eventually have their intelligence boosted to human levels (with Mrs. Frisby as one of the first among them to be uplifted, obviously enough).
Does humanity stand a better chance against the Rodents in this Rats of NIMH AU, or against the Apes in the rebooted Planet of the Apes series? Could humanity possibly win the coming fight of dominance? Could we co-exist in peace, and relative independence (as Nicodemus advocates doing)? Or would the Rodents rise up in their droves and out-compete us, driving us either into slavery or to our extinction (as Jenner and his faction advocate doing)?