This is an interesting little story and I enjoyed it. It's definitely different from all the other stories that focus on pokemon as if it were in real life. That being said I do have a couple critiques.
The story jumps around a lot and it's hard to follow your progress in the game. I wouldn't mind a little longer story if it patched up a couple of missing parts.
Make sure to start a new line whenever a new character speaks. It helps with making the story look more inviting to read and makes it easier to read.
You've got a nice little story on here with a unique twist most writers never think about. I just want you to get the most out of this story.