Ever since you've even started adventuring Hoenn, you've had to fight off Team Aqua on multiple occasions. All you're trying to do is get the eight Gym Badges and win over the Pokémon League, but you've also had to defend multiple people and places from the goons of Team Aqua. Their leader, Archie, is always talking about "expanding the sea" using an ancient Legendary Pokémon, but no one took him too seriously. Expanding the sea? As if a human could achieve that. That is... until Archie stole a submarine, and entered the Seafloor Cavern. Although you have other things to do, you know that you MUST stop him. He's gone too far. You dive down into the water on the back of your trusty Swampert, who swims as quickly as possible towards the Cavern. He even plows through an area that's caved in, giving you a shortcut... he seems to have just as much determination towards this cause as you do. You two eventually reach a large, open area with a lot of water, and Archie is there with Shelly, a Team Aqua admin. Archie appears to be holding some sort of red orb.

Archie: "Ugh... not this kid again... I'm in the middle of something!"

Shelly: "You're too late, scamp. The boss's plan is already in motion!"

You and Swampert attempt to do something about this, but a bright flash of red stops you. Almost immediately after, a gigantic, whale-like creature emerges from the water with a screech, going up towards Sootopolis City. Archie has a sadistic smile... until he gets a phone call.

Archie: "What is it, Matt? I'm reveling in my victory. Huh? What do you mean "Kyogre isn't listening"? What do you mean "Hoenn is flooding"?!"

Panicked, you and Swampert go to the surface. Every single Gym Leader, Elite Four member, and even the Champion appear to have rushed to the scene, doing whatever they can to keep Kyogre at bay.

Flannery: "WHAT THE HELL DID ARCHIE DO?!"

Norman: "I knew that man was absolutely deranged..."

Kyogre sees you, and screeches yet again out of anger.

Kyogre: "YOU..."