... the peace granted to the world. For many years they slept until one day the orbs were destroyed Why? How? They're guarded at the top of Mt. Pyre, aren't they?. The world was put in harms way and the sky master went mad Why?. In it's fury it turned black ...does it shoot out stars now, too? Either way, it's a cool idea if you have justification... and only one person from a little town in the Alora Wait, what? If this isn't in Hoenn, then...well, it has to be in Hoenn. Unless Mt. Pyre warped away, I don't get how this would carry out. Rayqyaza rests atop the Sky Pillar, ad Kyogre and Groudon are resting away in Hoenn, as well... region can calm it...
As a young resident of Treegrove Cherrygrove you head off to see the famous Prof. Eric Not that's an interesting name... of Regona city. When you get there though a shady character With a big R? bursts out of the lab's doors and takes off. Moments later Prof. Eric bursts out of the doors and asks you to help get his research back What's so great about stealing the professor's research? And these dudes and dutettes in academia are in a tightly-knit community; they will undoubtedly beef up security in eharing one of their colleagues robbed.... You agree and he gives you a Riolu to take with you Why Riolu?. The two of you brake off in pursuit. You track him down and battle him. The robber reveals himself as a member of team Magma Red flag: this evidently happens after RSE. That's fine, but I don't see what business Team Magma has here. If you're aligning with the anime continuity, they're even dissolved. Game, anime, or otherwise, Team magma saw what happens when they mess with Mother Nature--burning of Hoenn. Why would they go after the legends again? I don't see why else they'd be here...besides, without the orbs, how would they control them? They couldn't do it with the orbs.... He drops the research and runs...
You head back to the lab where your best friend awaits. Together you set off to places I am yet to think of, including the Lake of Rage Huh? How did we end up in Johto, dude? and Poketopia. Along the way you encounter team magma, team aqua, and team Aero, the new team representing the sky... somehow. You have explanations for this stuff, right?
Eventually though you arrive at Seabreak Peninsula. You travel over the peninsula in search of the entrance to sky tower Is that a Sky Pillar spin-off?. You enter and travel to the top where team Aero awaits. You battle your way to the top and faceoff against the leader of team Aero. You win and release Rayquaza who turns green and flies away ...so the leader and his black Rayqyaza were just waiting for you? I really don't get this.... In victory you set off toward victory road and League Hill.