*spoiler do not read below you have been warned*
The way I understand the story, is that Kadaj and his gang are trying to bring about the Reunion again. Cloud, and Tifa too, are part of a delivery service of some kind. Then, we have the Wheel-chair Man, who is Rufus. Rufus is in dealings with Kadaj, because obviously, Kadaj wants Jenova. Rufus knows where she/it is. So, when Kadaj starts to realise that Rufus isn't going to help him, and that he's just stringing him along, his attitudes chaneg. Rufus hires Cloud and the gang as bodyguards, and sends Reno and Rude with Cloud. Also, Kadaj then summons Bahamut to cause chaos and destruction in Midgar because of Rufus's unwillingness to help him.
As far as the whole geostigma thing that's going on, I've been trying not to spoil that for myself, so I don't know much about how all that is related; at least, not enough to post it here. But, what I said above, is how I interpret Rufus, Cloud, the clones, and the turks, and their interaction and relations.
