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If I knocked out mewtwo during the fight against him Am I doomed to never complete the pokedex? 

Since every attack was not efficient just like against his clone armies I though this was a boss fight and that I would be able to capture a weakened version (who wouldn't be not efficient against him on every type) of him after the battle. 

It didn't even cross my mind that I could capture him like that. 

At the moment, yes. I didn't think about it since I had a few opportunities to get a Master Ball, but I can make it to where it resets after beating the Elite 4 if you didn't catch him. It would just trigger the wild battle.

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That would be much appreciated. 


Worst case scenario is starting a new game when I do the update, but if that's the case, I'll send you a link to a copy specific to you for which other 4 Pokémon you want to start with at level 5. :)