I'm gonna get this off my chest now before the next chap comes out and ruins everything I've thought of. Just hear me out for now.
It all starts with this chap The dream Asuna has
And ends with this one what Fate says about her here
THIS IS ALL SPECULATION.......
What if Ostia was planning to take over the world using Asuna's powers (assuming she has another hidden ability) and had already started to subjugate/plunder other surrounding countries. In response to this the central government (mesembria was it?) and another underground organization (Takahata-san called it KOSMOS in this forum) decided to deal with the problem in their own ways.
Kosmos saw Asuna's existence as a threat to the magical world itself and planned to destroy her after capturing her(Hence Fate's words). The problem was their approach; They killed anyone who posed a threat to their mission and the mercenaries they hired (such as Canis Niger) tended to overdo things, which brought them to the central government's attention and branded them as enemies. The world government planned to seal asuna away once she was captured and wanted to destabilize Ostia's ruling family to prevent another weapon from surfacing.
Kosmos reached Ostia first and began attacking each island in turn. In order to prevent Kosmos' advance to their capital, Ostia sank their surrounding islands using Asuna's power: Killing thousands and leaving thousands more without homes. With Kosmos' main fleet stormed the capital shortly afterwards.
At this point in the war the red wing had encountered and fought against Kosmos' forces and learned their objective: one was to destroy asuna, and the other was to take her for themselves and use her. The Red wing defeated their fighters and destroyed Kosmos' hideout, finally ending their assault on Ostia. That brought the war to an end.
Though after hearing what the central government was planning for Asuna, Nagi decided to keep Asuna under his care. The government wasn't happy with this, and had agents sent after Nagi and the members of the red wing causing them to go their separate ways and for Nagi, Gateau,Takamichi, Alberio, and Asuna to live on the run.
Eventually the world government handed the job of retrieving Asuna to another organization that was rougher with their methods and didn't care for any damages done. This ended with Nagi's disappearance and Gateau's death. With Eishun's help, Takamichi and Asuna made it to the Human world and hid themselves in Japan.
Uh..... that's about it....I had it more thought out last week........ I shoulda posted it when it was still fresh....