Well we know the Garlean Empire is at war with the Primals. We can assume that fifteen years ago (thats when the opening cutscene takes place correct?) they had actually managed to capture them all and were transporting them when big dragon guy (I like to think its Bahamut) freed them, killing (or sealing or whatever) himself in the process.

Seem's pretty self-explanatory. In all likelihood it will still be there after 2.0 (maybe the events of the 7th Umbral Era will even wake him up?) So we can worry about that plot-line when we get to it. I doubt they would just ignore it forever.