The rat with the number, A-9, is Justin, Nicodemus's neighbour in the lab, and one of the brightest of all the rats. One night he confides to Nicodemus that he's going to look for a possible way of escape for all the rats, and next day, true to his word, when the scientists come to unlock the rats' cages for the daily experiments, he jumps out and runs around the place, looking for an exit. He explores the surroundings thoroughly, and eventually finds a way out, leading from the air ducts. However, the scientists don't realise that he's done this, as he is eventually returned to his cage.
Although the scientists were expecting sooner or later that one of the rats would try to find a way to escape, they think that Justin has simply learned that he cannot get out. Nicodemus observes they are quite wrong:
But they were underestimating Justin. He had learned no such thing.
The key word here is 'underestimating'. Although Dr Schultz and his colleagues aim to increase the rats' intelligence, they fail to realise just how intelligent they become, in an amazingly short space of time. It is not long before Justin and Nicodemus lead all the rats out of NIMH, to start a new life of their own.
The rats have acquired super-intelligence, but they are left at something of a loss as they try to figure out their new place in the world. They are now far too advanced to revert to their old ways of scavenging among bins, they cannot fit in with other animals but they cannot assimilate with humans either. They are really on their own.