Well, if the main sites timeline is correct, then the game has to do with Vane rising to the sky and the actions of the Magic Empire.
966B At this time, a Magic Empire rules the world. Again, according to TSS.
966B The Magic Empire revolted against Althena and tried to conquer the world. Again, according to TSS.
966B Because of the evil deeds of the Magic Empire, Althena was saddened, and her tears fell for 7 days, causing a great deluge, purifying the world, and crushing the Magic Empire. Their ruins cannot even be found today. This deluge caused Vane to rise to the sky and become the center of magic for LUNAR. Screenshots from the TSS Library: 1, 2, 3, 4 and 5. This has been confirmed as 1000 years prior to LUNAR 1, based on a number of references in TSS.