Walkthrough: By heading through the door to the left, you will encounter numerous warp pads that lead to various different areas, all of which will hold Team Rainbow Rocket Grunts ready for battle. The goal is to find the room with the Team Rainbow Rocket waves of blockades, making your way past all of them to ultimately find the room where the Leader of Team Aqua, Archie, awaits.
From what he tells you, Archie has been brought from a universe where he was actually successful (or so he says) in causing the Hoenn Region to flood in order to create a world where Pokemon can live free. It isn't clear if he was never defeated by the heroes of that region or if he had yet to face them, but he'll say he was pulled away right as he was successful in fulfilling his plans. He doesn't know how he got here, but he plans on doing the same exact thing on this planet.
Team Aqua Archie - Level 64 Mightyena, Level 64 Crobat, Level 64 Muk, Level 64 Sharpedo, Level 66 Kyogre
After defeating Archie, you will need to press the button behind the painting on the back wall in order to continue onward.