Storyline? You think I'd come up with all this and NOT have a storyline? Here itis(it's pretty damn long):
You start in Cleanslate Town. You have the typical goals of beating the gym leaders and the elite four. In the intro you hear about this fight between Team Galactic, who have come from Sinnoh, obviously, and Team Aero, from Hoenn. Team Aero was founded by a trainer in the Hoenn region when Team Aqua and Team Magma were fighting. This trainer had decided that they had enough with evil organizations and would counter with their own. Their main legendary was Rayquaza, and when Groudon and Kyogre were fighting, Rayquaza was awakened to save the day(events from Pokemon Emerald). At any rate, you don't actually see any of this until you reach the 2nd gym. After beating it, the leader of Team Aero shows up, talks about the fight, says he will appear throughout the region to test your skills(he will become your rival as well as your ally), and battle you. You progress in the game. After the 4th gym, you are directed to Team Aero's headquarters. You, as the trainer in the storyline, don't know that Aero is good, so you fight 14 grunts, 2 Admins, and the leader. He then talks to you and sets you straight. Later on, you encounter some Galacitics outside Seacoast City. You hear their plot to control Arzeus, the Omega Pokemon(more powerful than Arceus). So after hearing this, a bunch of Aeros come and ask you to help them catch the regis(there will be some new ones), and they will give you a master ball to catch each of them. The only things with that is, you have to give the regis to them. You also have to track down the 3 legendary birds, but this time Team Aero will catch them. Then, they set you back on your journey after giving you an HM. After the 7th gym, however, you hear that a new member has joined Team Galactic. They quickly became a Commander. You also hear that Dialga and Palkia were captured by Team Galactic. Team Aero is chasing Giratina to beat them. You hear all this from a Kanto trainer is not revealed(he turns out to be the champion). You go to Mt. Kosmo, where you find some Aeros fighting Galactics. Beat them and go on. You help 2 Aero Admins beat Commander Mars and Commander Saturn. You reach the summit, and all admins and commanders, as well as some grunts, come too. Cyrus and the leader of Team Aero are already there. It's there you find out that the new Commander Neptune was once Aero Admin May. As a result, Team Aero's leader will not face her. Instead, All Aero members take on the Galactics. He then battles Cyrus, temporarily stopping the awakening of Arzeus. You battle Commander Neptune. After the battle is over, all of Team Galactic's Commanders and most of its grunts were beaten, but somehow Aero's leader lost to Cyrus. As he heals his Pokemon, Cyrus awakens Arzeus. An Aero grunt runs in and shouts that the region is in chaos, and will soon be destroyed. Galactics don't give a crap. They let out Dialga and Palkia to start making an new universe. Then Aero lets out their surprise weapon, Mesprit, Uxie and Azelf, who stop Dialga and Palkia. Team Aero then unleashes Rayquaza, all the regis, Giratina and Mew. Then, out of nowhere, Arceus appears and joins Aero's little army. Arzeus is beaten, and returns to eternal sleep. Cyrus is pissed. He yells at Commander Neptune, who is upset for a number of reasons. But she reluctantly listnes to Cyrus and temas up to beat Aero's leader. Aero's leader heals your Pokemon, and then asks you to join him to battle the two Galactics. You have beaten Team Galactic. For now. They return later on. Everyone leaves Mt. Kosmo. You go on and beat the last gym, but before you can face the E4, the Aero Leader is back to test you skills one last time. Beat the Elite 4, and then the Champion, Ash. That's the end of the pre-E4 game.