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?
Okay, so here is my idea (another epic idea to come from showering:p):
The story will take place 3 years after the defeat of Gary at the hand of Red. Gary was so distraught by his loss that he travelled the world looking for ways to become stronger. He tried new battling styles, trained under gym leaders and with former elite fours, and even experimented with new kinds of protein and iron. However, he could never overcome Red. No matter how hard he tried, Red always won. One day, he came across a group of scientists that believed they could successfully make a Pokémon stronger through genetic manipulation. Gary jumped at the chance, offering up his "worthless" charizard as a trial. The experiment goes horribly wrong and Derpizard is formed. Gary, who breaks down in tears, grabs the Pokéball and runs off. The scientist all run after him and tell him that they can fix it. After a second failure, Charizard is soooo pissed off and derpy, that he fries Gary. Unknowing, in the second attempt, a virus that was within Charizard was also mutated. This mutation allowed it to completely replace the DNA of any cell it met with its own: the DNA of Derpizard. When Charizard fries Gary, this super-virus becomes airborne. Gary is the first to succumb, and the scientists are next. It slowly makes its way through the region, affecting everyone it comes in contact with. There is no cure.
Here is where the player comes in. He witnessed everything that happened, but due to the door being closed, had enough time to get away. He dons a gas mask and decides he must find a cure. He was on his journey to collect all of the badges when he witnessed this. He hopes that the only person who has enough experience in the world to guide him is the Champion, so he forces his way to Indigo Plateau. When he arrives, he finds it a maximum security section: (by this point, the virus has spread throughout all of Kanto and Jhoto, it has barely made it into the Orange Islands and the Sevi Islands due to boats, and finally, Hoenn, Unova, and the Sinnoh reginion are close to being infected. It is slightly after this time period where Pokémon Derpizard actually takes place) and the only people left in Kanto, besides the hero, are those withen Indigo Plateau. He is forced to go through 5 separate cleansing chambers before his entrance is admitted. When he makes it inside, he is offered an audience with Red almost immediately due to the fact that he is the first outsider in well over over a month. He discusses with Red what course of action they should take (i have no clue here, help me out.... Yada yada yada;p) and in the end, a cure is found, and as the hero completes his journey to gather all of the badges, he spreads the cure and soon the situation is solved. Something should also happen with Gary and the scientists.