More likely it will be a reference to the parasite come to be known as Jenova in Final Fantasy VII. If you did the side content involving Aeris's mom in the original game, you know that this parasite was referred to by the Cetra as, "The Calamity from the Sky."

What this parasite did was take over life on the planet, eventually consuming and mutating a Cetra known as Jenova, giving her the will to dominate the planet.

Which I mean, in itself was a call back to Chrono Trigger with Lavos dominating Queen Zeal's will, but even with the advent of the Black Omen, she did not take over the planet or even adjust history really.

We gotta consider that when Zodiark went up against Hydaelyn, the planet got fractured on the space/time level, splitting into 14 separate instances of the same reality. No idea how a Lavos-like/Jenova-like would really play into that, beyond the initial calamity, given there's been no real sign of them this whole time.