They didn't "invade", they were just let out of that secret l'Cie training camp you visit in Chapter 11. They were already there and stored someone, presumably Barthandalus, just had to let them out to cause havoc. They were released as part of a coup, so that the Sanctum forces would either kill Orphan themselves, or force Lightning and Friends to intervene to try save Cocoon from being destroyed (Ironically, by destroying it themselves first).
As I understand it, Eden is Edenhall, the actual building where Orphan is kept hidden. I presume they're separate entities because one is hiding the existence of the other.Why are Eden and Orphan separate characters? From the perspective of a story writer, they both serve the same story role--the entity that sustains Cacoon--and could simply exist as one character. It's one example of the many needless over-complications in the story.
That's right. The explanation is quite literally "a god did it!". A god which you never actually get to see in game at all, and is only mentioned very briefly just before you go back to Cocoon. Whats worse is that they don't even bother to tell you that a god did it and just leave you wondering until you go look it up on a Wiki somewhere. It may be expanded upon later in the trilogy, but I get the impression that at the time the writers themselves didn't even know what they wanted to happen and had to retcon something in later to advance the story enough for sequels and just decided to have their deus ex machina ending be justified by pointing out that it is deus ex machina.In particular, the ending makes no sense. It is deus ex machina stacked on top of more deus ex machina.
Which just further emphasises the writers lack of direction. If you need to explain things again later then chances are you did a very bad job the first time around. Either you were unclear in your original presentation or you didn't know yourself what was going on. Both are equally bad when it comes to telling a story because they lead to horribly convoluted and misunderstood plots at best and deus ex machina endings at worst.