In the beginning of Shinsekai Yori I didn't suspect bakenezumi's thread would be used as a important theme. In the end I'm happy it did, because it lead to interesting aspects. I will try to analyze some of bakenezumi's life through these years, it will be more of summary and if you watched the anime more carefully than me, you can amend me if I made a mistake.
Spoilers till episode 21 of Shinsekai Yori
Let's start with what exactly is a bakenezumi. They were born due the cantus leakage outside the barrier. The barrier (marked as a shimenawa) protects everything within and the cantus has no place to pull out but outside. Notice that outside there aren't any normal animals like we know, just mysterious creatures like bakenezumi and minoshiro. Bakenezumi lifestyle and breeding are similar to bees- the create colonies and have a queen who give birth to all of them. That's the side effects of cantus leakage. We don't know how humans reacted to bakenezumi in the beginning of their life, but we know how are they treated in the century when the title take place. For bakenezumi all humans are godlike creatures and humans use this privilege completely. The have almost ultimate control over them. They are gods, observers, researchers and judges. When a colony whats to battle another colony, their mediators must write a finding. That isn't showed in the anime but I suspects the same goes with many aspects of their life. When the battle begins humans observes the colony and take notes like observing a glass anthill. Obviously when a colony must write a finding one of them serves as a mediator and has learned human language and writing and one of the mediators of Robber Fly colony- Squealer is an important character in the story.
Saki and her friends meets Squealer several times and through the years his position and look changed. When we first encounter him he is a bakenezumi whose status isn't very high but since he is a mediator his more important then other bakenezumis in his colony. To her queen although he don't play any important role. Squerel in first glance is faithful to humans who he calls 'gods' but when he got the chance to make use of their power to his benefits he don't hesitate. Who's more easy to manipulate then the children? He's scheming bring out his colony to a better position eliminating the opposite colony thanks to Satoru's cantus. Some years later we see Squealer as he obtain the name Yakomaru. He was in a important position that he implemented more democracy rules in his colony, pushing off the position of the queen to breeding only. Where did he learn the conception of democracy? Surely not from observing humans or from humans themselves. He must obtain some source of information. In that times humans should start suspecting that something bad is going on. Than several year later Yakomaru continue to climb to more powerful seniority. We can see how he talks to humans comparing to Kiroumaru and how he looks. When Kiroumaru answers humbly wearing simple cloth, Yakomaru scheming building up his ego. Notice that Yakomaru is wearing some kind of golden collar looking like a king. At that time he thinks himself not only as a mediator between bakenezumi and humans but as a ruler. Again humans should notice this change of approach, all the more that Robber Fly colony started to use very complicated weapons like guns. They had to got some source off information.
For humans it was shocking that bakenezumis strike them, killing someone their earlier called gods. Bakenezumi are intellect creatures but I doubt that they were concerned so much about living as humans pawns. Surely for them living this way was very unjust but I think living in a colony was more important to them. When they got a leader, a good strategic with important information, that is Yakomaru, something lighten up in them.Yakomaru answered to that what they desired or rather what they should desire in his mind. He is trying to make bakenezumi rule the world but moreover he is trying to be a king. A big ambition and big ego lead to war between humans and bakenezumi. However even a army of bakenezumi isn't enough to defeat humans and their cantus. Yakomaru decided to rebound on humans with their own weapons creating a fiend.