Hmmm, so what i am thinking is that the player gets about 3 gym badges, and then "accidentally" walks in on Green and the scientists. Here, Green is explaining to them why he wants this so much. So, this is where the charactor finds out what has happened up to this point. Then, the experiment; fails. After another badge, he sees Green and decides to follow him. He meets the scientists who persuade him they can fix it. It is this second experiment, the virus is released and over time (how should this be measured?) the mutations get worse.
For the other pokemon, what if this came after the credits? Like, you think it is over, but then you come across that mutated pokemon, and it is like a Goosebumps ending. Possibly leaving it open for another game. What do you think?
*strokes chin in thought* yes, yes, that may just work.:p Then, we can use JPAN's wild switch routine to swap out pokemon based up on a variable, the high the variable, the more changed the pokemon are.
Sorry, I haven't had much time to think of ideas for the story, but I do have one idea you may like. What if we fuse pokemon sprites with parts of Derpizard to show the transformation process starting?