Ruby is losing friends by the minute...! Why does Sapphire never want to see his face again? And why has one of Ruby’s Pokémon run away? Meanwhile, the Hoenn region is on the verge of destruction as two Legendary Pokémon clash in the depths of the ocean—and only Ruby knows how to reach them to intervene!

Then, what will happen when evil Team Aqua and equally evil Team Magma team up?!