Team Aqua had achieved their goal. Most of Hoenn had been flooded, leaving only the highest parts of land above sea level. Aquatic Pokémon thrived - enjoying the space and freedom they had, especially with most of humanity residing in other regions as opposed to dealing with the new Sea-filled Hoenn.
And as a result, Team Aqua split up, for the most part. Some left to leave for other regions, while others helped in making civilisation on what land remained so that the humans who remained could survive and thrive with Pokémon. It was also safe to say Team Magma had left the region as soon as Team Aqua had started winning.
Then there's Archie, the former leader of Team Aqua. Still sporting his Team Aqua attire, including his blue bandana and wetsuit which he had the top half taken off, left behind him as his muscular torso was revealed. He resided by the shore of one of the few pieces of land left. Sitting on a rock and feeding Kyogre one last berry before seeing it off for the day, he sits there, admiring the sunset over the ocean he helped create.
"Ah... Another fine day in paradise."