The Wild Beyond by Piers Torday

This is the story of a boy named Kester. He has rescued the last wild animals in the world, and saved his capital city from destruction. But now he must face his greatest challenge yet, because:

1. The only blue whale on the planet has brought news from across the ocean
2. A mysterious steel dome has risen from the Four Towers
3. Out there, somewhere, a brave mouse holds the key to the future...