The Logic is ruined....
Based on the pic I drew http://isapphirus.deviantart.com/art/Our-Love-is-Powerful-Pokemon-ORAS-500169974 this is part two kinda LOL.
Rayquaza realized he wanted some attention for the Holidays too, wanting them to battle so he can save the world again, so he tries to make the poor couple's lives a misery, and yes, Groundon and Kyogre are named Groudin (male) and Kyogie (Female). Also, yes, Groudin's running on water. xD