It is confirmed that Groudon and Kyogre are still in existence even after (SPOILER ALERT) Rayquaza nearly kills them with it's hyper beam. Alain is on a quest to calm Groudon and Kyogre
Here is how I think it will go.
Kyogre and Groudon (No Rayquaza) relocate to the Kalos region. Then a big battle engages between the two massive titans (Kyogre having the advantage this time). After fighting for a while they awaken Zygarde. Zygarde will fly out from the ground and then mega evolve (or primal revert) much like Rayquaza did, (also this is where they would show Yveltal awaken much like they did with Groudon and Kyogre in Act II) Zygarde stops Groudon and Kyogre almost instantly and then reverts back into its normal form and goes back to sleep. Alain then continuous his journey to defeat all mega evolutions.
Here is how I think it will go.
Kyogre and Groudon (No Rayquaza) relocate to the Kalos region. Then a big battle engages between the two massive titans (Kyogre having the advantage this time). After fighting for a while they awaken Zygarde. Zygarde will fly out from the ground and then mega evolve (or primal revert) much like Rayquaza did, (also this is where they would show Yveltal awaken much like they did with Groudon and Kyogre in Act II) Zygarde stops Groudon and Kyogre almost instantly and then reverts back into its normal form and goes back to sleep. Alain then continuous his journey to defeat all mega evolutions.
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