This is where we'll discuss what's going to be the main plot of the story. Feel free to post up any ideas you may have here.

So far there have been a few suggestions.

While Celestia is either dead/in a coma due to the castle collapsing underneath her during the Canterlot storm, Luna's fate is more ambiguous. When the storms started hitting, she and some of her guards went in search of a way to stop them in the form of the magical heart of the world, the Nexus. The last thing they heard from the expedition was that they had found it, along with a rough guide of how they got there, with promises of a more detailed report once they knew more. This was the last anypony heard from Luna or any of her guards.
The newly returned travellers can then search for the Nexus and find Luna, helping to bring back some stability to Equestria and the world beyond.

Transferring the arc ideas across from the other thread.

Hmm… possible arc ideas:

First arc - return of the warriors, possibly hooking up, finding out what happened to them/Aedrides, start bringing back a central government and clearing the nastier trouble spots, and find out about the storms

Second arc - Continue government establishment, find out that the storms might (probably will) come back and likely affected more than their world, find out about Luna/Celestia/others, start expedition to find the source point

Third arc? - Return of immortals (Luna, etc), Aedrides starts to settle, but possible effects elsewhere seen, maybe some start searching other dimensions for those still missing or to help those still having storm problems.

Fourth arc? - Start of inter-dimensional/planetary relations and return of those still lost

'Nother plot point someone might want to look into, the Equestria Girls world, particularly with regards to Sunset and her reaction to losing contact with Twilight and what happens to the mirror-portal.