I think something a lot of people are missing is -

Whatever caused the Final Days was, to the best of our knowledge, terrestrial. The starshower heralding the Final Days was just a symptom of the Sound, not the source of the issue itself (a la Jenova or (to my knowledge) Lavos). The real issue came from within the planet itself - or, perhaps, the aetherial sea.

Aside from the commentary of the various Amaurotine shades explaining the Final Days, the final boss of the Amaurot dungeon (Therion) bears the title "Chthonic Riddle." The word "chthonic" literally translates to "subterranean" from ancient Greek, but in contemporary usage refers to deities and spirits of the Underworld. Considering the Ancients referred to the aetherial sea / lifestream as the "underworld"... you can put two and two together.

My train of thought may turn out to be wrong (it has been before), but whatever actually happened, I doubt it's something so simple as a hibernating malign alien that crashed on the planet millennia ago suddenly acting up.

Regardless, we're unlikely to get answers for that specific event for a long while; 5.3 is the culmination of Elidibus' hastily cobbled together plot to be rid of us, so he's liable to be front and center. I'd not expect to see the issue addressed until 5.4, at the earliest.