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?