Widowed fieldmouse Mrs. Frisby turns to the rats for help when her family's house is threatened, only to find them abnormally intelligent and with technology. They reveal that they knew her dead husband and they help her and her family before they leave the farm for a new life free of the technology they feel they depend on too much.
On the surface this is a child-friendly story in which a widowed fieldmouse seeks the help of her friends and neighbours when her family's house is threatened by the farmer's plough. When she helps a young crow escape the cat, he rewards her by helping out on several occasions, in particular taking her to see the owl who suggests a solution and points her towards the rats, who carry out the owl's idea. On the way, Mrs. F. overhears a plan to smoke out the rats, which she passes on, making sure that they escape in time. A neat quid pro quo, neighbourliness and friendship are all satisfied.
But then we enter the subplot of the titular Rats: escapees from NIMH - some sort of bioengineering research facility where they were experimental subjects injected with DNA to enhance their intelligence. Their treatment was not harsh but did include the usual cages and electric-shock mazes. The experiments were more successful than the researchers realised, and the rats escaped, along with some similarly-enhanced mice. The escaping rats and mice overcome hardships until they settle in the a farmer's garden where one of the mice, Jonathan Frisby meets his wife and starts a family. The rats use their new-found knowledge to build a rat-burrow provided with electricity, running water and a library, scavenging from the nearby house and garden. At this stage, we seem to be looking at a sort of mixed parable concerning animal experimentation in general, bioengineering in particular, and a suggestion that perhaps rats are innately smarter than humans. There's a short section in which Nicodemus explains that it was more-or-less an accident of nature that gave humans the upper hand over other creatures.
When you look again, you realise that for all the rats' technological advances, all the animals are basically intelligent. In common with Beatrix Potter, The Wind in the Willows and many other books, the animals all live effectively human lives, only in a more brutal milieu. The animals have a normal humanesque family life, but Mrs. Frisby is still worried that the owl will eat her when she approaches him for help. (The only apparently unintelligent animal is the cat, the animals' common enemy). The rats' search for a better life without the technology they feel too dependent on, and without stealing from the farmer, is far more a human quest. To our modern eyes, it represents a yearning for a simpler, more moral life: the rats have acquired a conscience along with their intelligence. Interestingly also, the few humans encountered throughout the story are not despised by the animals, nor accused of crimes against Nature. True, the rats escape from the scientists at NIMH but there's no attempt at moral superiority. Tim Golden is a computer programmer living in London.  He is also the editor of the Good-to-Read website.