This was a series I read probably almost a decade ago after borrowing it from the library, and at the time I recall the third book was still being written. It involves some mice spying and doing secret operations within a dictatorial country of mice. I also recall that mice of a certain color (ginger?) were being discriminated against, so it may have also been an allegory.
I also recall that using birds for transport may have been a plot element, and there was a Hamlet reference involving skiing while holding a tree in front of you.
Now that I'm thinking about it, I believe one of the main characters was named Alistar. I'm not 100% sure on that though. Any leads, or help finding it, would be much appreciated; it's been nagging at the back of my brain that I don't know what it was called. I'll do my best to answer any questions.