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My level 56 Dragonite killed a level 70 Rayquaza, and for some reason I can't progress in the game! P.S I am on Alpha Saphire

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With Rayquaza having regained its power, the player must capture Rayquaza to take control of it and save the world; if the player runs away, defeats Rayquaza or is defeated, Rayquaza will remain and be ready for battle again fully healed (its Nature and IVs reset each time). If the player has no Poké Balls, Zinnia will give the player an Ultra Ball.