Story

The story starts out in GBA graphics as you see Professor Birch on your screen welcoming you to the Pokemon world exactly how he did in Ruby and Sapphire. Then, you come back into the 3d visuals as you step out of your truck and look around your new town that you'll be living in. As soon as you get to control your characters your mom tells you to go to Professor Birch's Lab where his assistant will tell you that he's not there. You later go on to Route 101 where you see the professor being attacked by a wild Poochyena. He tells you to pick one of his starter Pokemon and after you pick one you battle against Poochyena. Once you save him he tells you how grateful he is and sends you along your way. You later come back to him to recieve a Pokedex and meet his daughter May. Then you go on to different cities collecting different badges and battling your rival May multiple times. You also discover the threat of Team Magma or Aqua depending on which version you're playing and you need to stop them from awakening Primal Groudon or Primal Kyogre. You meet a man named Steven along the way who is also very interested in Mega Evolution. Once the legendary awakens you have to go and find it and then battle and capture it. Then once you recieve your 8th badge you go on to the Pokemon League where you battle the Elite Four and the Champion, Steven.

Delta Episode

After you beat the main game, the Delta Episode starts where you meet a character named Zinnia who steals everyone's Key Stones in order to summon the legendary Pokemon Rayquaza in order to stop a meteoride from crashing into Earth. You chase after Zinnia all over the place until you reach the Sky Pillar where she tells you a story of her people, the Draconoids, and how they could control the ultimate power of Mega Rayquaza to save them from disaster. Zinnia later summons Rayquaza on top of the Sky Pillar and you have to fight it and capture it which then leads off to Rayqaza being able to Mega Evolve based on your will. Then you and Rayquaza fly off into space to destroy the meteoride. From that Meteoride emerges Deoxys, the DNA Pokemon, where you can battle and capture him also.