Okay to tell the truth, I really didn't get this story but I'll try my best.
There were two types of animals that were in this video; the cute ones, and the gray-ish ones.
Like everyone said, the cute one is most likely the main character. Both animals represent human, but they end up in a different place at the end.
The cute varmints loved nature and valued it. However, those gray and sad looking varmints came and they started destroying the environment by constructing huge buildings and factories that emit black smoke in the clean air.
I thought that the gray varmints represent people who don't cherish the environment, and the kind varmints represent people who do.
I didn't understand what those jellyfish looking things were, but I thought that it was a place where only the varmints who took good care of the environment gets to go. Meanwhile, the earth eventually gets dirtier and polluted so all the gray varmints start to die.
So, I thought that this video is probably predicting that we should do things to save the earth or else we will end up like the gray varmints.
