Jenner is worried first of all about the consequences of the experiments that have been performed on the rats in the laboratories of NIMH; he is worried about what exactly the implications are for rats who have human intelligence. He says,
"We don't know where to go because we don't know what we are. Do (we) want to go back to living in a sewer-pipe? And eating other people's garbage? Because that's what rats do. But the fact is, we aren't rats any more...I think we can learn to do anything we want. But where do we do it" Where does a group of civilized rats fit in?"
Jenner's intelligence has increased to the point that he truly is able to see the big picture, and all the various ramifications of what has happened to them. In addition to worrying about the rats' new identity and their place in the world, he is concerned also about what the reaction will be when the news is spread that "there's a group of civilized rats roaming loose - rats that can read, and think, and figure things out" (Chapter 18 - "The Air Ducts").