The main character and the other varmints are living happily on the prairie when some sort of industrial revolution happens and the entire place is covered with concrete skyscrapers and thick smoke. The main character takes care of the last surviving tree, which releases seeds into the city. Then, those seeds grow into aliens with a biome within them. The varmints then continue living inside the aliens.
Analysis:
I believe this film was trying to show us the true horrors of environmental damage and destruction through the eyes of small creatures.