How is Giratina doing this controlling, by the way? Mind control? It's not a Psychic-type and doesn't seem to demonstrate mind-control powers, as far as I know. Why does it decide to use Blank Division and Neo Galactic as puppets anyway, and what does this puppeting involve? Causing them to fight each other and destroy the world themselves? Do any of them ever realize they're being controlled?
And, while this is a minor thing, it's probably worth pointing out: Cyrus never went to jail. In Diamond/Pearl he just... vanished, pretty much, promising to come back. He wasn't arrested. You could just have him in hiding for a while and then come out of hiding to re-form Team Galactic instead of escaping from jail, unless it's somehow important that he actually be arrested and jailed at some point in the ten-year gap between Diamond/Pearl and your hack.
1. They were created after Galactic was disbanded, and the Blank Division blocked off the region from the world.
2. Giratina is using Darkrai to corrupt their minds in their dreams, basically, since it is still trapped, and only other legends can get to where he is for most of the game, at least until its portal opens up. And at the end, one of the leaders of the Blank Division realises that he was being used, but doesn't care, and tries to kill you anyway. Giratina's manipulating the leaders to do his bidding, and it involved cutting off Sinnoh from the world.
3. It actually is kind of important for him to have been arrested, as then Galactic would disband for the first time, and allow the Blank Division to move around more.
4. The Elite 4 can leave, the leaders of the Blank Division won't stop them. And I guess they don't really notice because Giratina's influence blinds them to that fact. (Actually, technically it's Darkrai's influence) They're meeting with the foreign regions to make alliances with them, so the backlash from defeating a man with a lot of supporters doesn't tear them apart (Because there likely would be some), as well as to have support in case of some other threat.
Yes, it and Darkrai. Giratina ordered Darkrai to influence specific people to do its bidding, and he's in the Torn World, only he can't get out of there.
I hope that answers your questions, I had a hard time getting a couple of them, but... I'm open for questions and ideas, for I'm still at that point... remember, don't expect anything for a long time.