When Nicodemus had been killed, his own soul was sucked into the Stone, where it was able to communicate in some way with the soul of Edgar. They merged, and together, they were placed into Edgar's body, and while they are still partially separate, over time, they will merge fully into a single individual. Before the Council, Edgar takes his place again as the undisputed head, radiating a new authority and confidence, courtesy of the Nicodemus part of him, and officially lays to rest any plan for war on humanity. He tells of the Rats of Thorn Valley, and what they did for him, and asks for the council's help in providing a suitable reward. They agree that some sort of repayment is in order.
Clouds gather, and to the surprise of all, rain begins to fall.
Light seems to come from the ground itself, and a blanket of green spreads over the surface as crops that have failed to grow suddenly revive, and in a matter of moments, reach their full height. Justin, Mrs Brisby, and all the other rats, look up into the heavens, with the rain down their faces, and with new hope for the future, prepare for a huge harvest.