In ancient times, two Pokémon fought each other in a great battle. One Pokémon, Kyogre rose waves and expanded the sea; the other, Groudon, expanded the land and rose plateaus. Their battle never seemed to end and the world was engulfed in the destruction the battle caused. One day, the two Pokémon stopped fighting and went to sleep at the bottom of the sea and have stayed there ever since.
In present day, the sea level rises, causing it to crash onto land until it nearly engulfs it. In Lavaridge Town, an Absol watches as people panic as their town begins cooling from the suspension of Mt. Chimney.
Back at Mt. Chimney, Amber is amazed at the power of the meteorite that allowed their machine to stop the volcano. With their mission complete, Team Aqua make their escape, taking Professor Cozmo with them. Sapphire follows them into the cavern that Amber's Carvanha opened inside the mountain, but Flannery is left outside. Underground, Sapphire tries to find where Team Aqua went, but finds herself being attacked.
Swearing to avenge Mt. Chimney's activity suspension, Flannery tries her hardest to revive it using her Pokémon. Suddenly, however, a voice behind her tells her that it is simply not enough heat energy to get the job done, and Flannery finds herself joined by a mysterious stranger—Tabitha of Team Magma. Although Flannery mistakes Tabitha to be a member of Team Aqua, he assures her that he is an ally and he is here to help try and revive the volcano.
Using his Torkoal to burn coal, Tabitha creates a powerful ball of flame and has Flannery add more to it. They fire the ball into the volcano, creating a huge explosion that destroys Team Aqua's machine in the process.
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