Well, mainly its about the legendary pokemon and Arceus.
As a character, you are a human from the human world who is confronted by a pokemon. Kidnapped or not, they end up taking you to their world, and you have a decision between fighting Arceus or protecting him.
In the world they live in there's no humans nor trainers, but they need you to help them, and harness their power. It'll be better explained once you see it.
You get to choose which pokemon confronts you, and what side you want to be on.
Well, I thought that if Althalos took a shiny umbreon, it might as well have been Lydia, since they looked exactly alike and they had no way of knowing she was in her illusion.