I'll give you an explanation in lee man's words:

The opening cutscene is a premonition of the catastrophe.
The catastrophe being the empire's plans to summon this huge meteorite to crush against the planet and purge everything.
We destroy the device they use to attract it, but its too late. So we have a back up plan to pray to the 12 gods to stop the armaggedon.
There's a final battle between the empire and the alliance of nations in mor dohna (to where the meteorite is headed).

We find out then that the meteorite is in fact a cage. Holding the god dragon, bahamut.
The empire has been feeding it aether energy so its stronger than before.

Thus the twelve are unable to seal him once again, and our plan fails.

So the reincarnation of the god of space and time sends us beyond the reach of time. Thus saving us from dying.

This plot wasn't the original one. It was shifted and molded by Yoshi when he took over.
There are some unfinished plotlines left by tanaka which might resume on 2.0.