I have not a clue how exactly it fits into the story line, but I know a bit. Cyrus in attempt to do somthing warps both Dialga and Palkia to Spear Pillar. At some point, Giratina warps there to do somthing (perhaps to stop Cyrus? Or just a visit?) and is obviously in Origin Forme when you battle it. Here's a website that has a bit of info on it:
http://bulbapedia.bulbagarden.net/wiki/Pok%C3%A9mon_Platinum_Version
Inactive for a full year. Now I'm back. Kinda...
"I control my thoughts. My thoughts control my emotions. Therefore, I control my emotions..."