@Jimera0, nice finish! A little anticlimactic though, although I like how you referenced the glitch earlier on. Next scramble will be just as awesome, I hope!
@IAR, actually Female with -Def is actually one of the better possible combinations (Leech Life and Toxic), might be able to stall stuff out. Don't feel too down.
AND I'm reserving for Terrador.
Terrador, take Mutant the Doduo. Doduo is one of the weirdest pokemon. What is this thing? A bird with two heads? BIZARRE! It must be a mutant. And like most mutants, it has strange and remarkable powers. Teach Mutant Fly and Steel Wing, even though it has no wings, and keep those moves forever. Mutant hates all other mutants for some reason, so have it solo 15 other mutants to evolve (that is, any pokemon that you judge to be a mutant, no particular guidelines here.) However, it does feel a certain kinship with others like it, so it may not KO any pokemon with multiple heads. After it evolves, Mutant grows ANOTHER HEAD! Crazy! But what's this? This special third head has memories of its past that the other heads forgot... Mutant is actually an experiment created by Team Rocket! Mutant is enraged by this. So, Mutant must solo 15 Rocket Grunts, and Giovanni at both Silph Co. and at the Gym. Mutant can only faint 3 times (including retries) for each of these solos- one for each head. How well Mutant does in these solos determines its further restrictions;
-If you fail to solo Giovanni either time, Mutant loses the ability to use STAB moves except Fly, since Mutant thinks that restricting itself will help it get stronger. It should also solo 2 of Lorelei's pokemon, because Ice is strong against Flying, and that should help Mutant improve.
-If you fail both times, Mutant loses the ability to use STAB moves except Rage (you must keep Fly on its moveset, but it may not use it in battle), and it may never use a super effective move, because Mutant is angry at itself for being such a failure, so it punishes itself. No further restrictions because Mutant sucks now.
-If you succeed both times, CONGRATULATIONS!! Mutant gets a new lease on life, and aims to make itself better than ever! How you may ask? By challenging the Elite 4 of course! Take he number of times faints Mutant was still allowed from its final battle vs Giovanni (maximum 3, minimum 0).Take this number and +5. That is the number of E4 and champion pokes that Mutant must solo.
Whatever happens vs Giovanni, Mutant hears about another Mutant Team Rocket created. In fact, it's said to be the most powerful pokemon ever! Looks like Mutant just got one final challenge. Solo Mewtwo!!
Edit: user 18, I am still loving your updates! If the pokemon world was real, this is how I imagine it to be like. Also, I like how you portray Onix as being small while young- I hadn't even considered that. Go Rubble!