Pokémon Adventures, Vol. 20 by Hidenori Kusaka

Legendary Pokemon Kyogre and Groudon are unleashed and the world descends into chaos! Ruby and Sapphire head down to Seafloor Cavern to try and stop them. To make matters worse, Amber and Maxie, the leaders of evil Team Magma and equally evil Team Aqua, are controlling Kyogre and Groudon with the Blue Orb and the Red Orb. Or are the legendary Pokémon controlling them...? Meanwhile, has Wally built up his strength enough to train with Ruby's father, Gym Leader Norman?