I'm not in love with the modern world

We believe that:
All Pokemon are essentially the same species of creature. The original Pokemon organism was a microbe from space that infected various plants and animals, but rather than propagating like, say, a virus it "borrowed" chunks of DNA and grafted them onto itself. Now, while there are still some normal animals, most have been driven to extinction or close to it by their vastly more powerful/intelligent Pokemon versions. This is also why vastly different types can interbreed with ease, and why all types lay eggs despite being mammals/mineral/plants/etc. The plant types, interestingly enough, have largely retained their ability to reproduce via seeds. Ditto is essentially a very large version of the first organism. The Pokerus is the original strain, though perhaps "deactivated" as far as it's ability to cause hosts to give birth to DNA thieves. It's only a matter of time before humans banging Gardevoirs and Glaceons or whatever end up bringing about a human Pokemon which will herald the extinction of man.