When Emet said the sound emanated within the planet one of the first things that came to mind was Lavos. while again I doubt it would be a 1 for 1 recreation it might be a being partially inspired by Lavos or Jenova, a parasite from beyond the stars that wreaked havoc on the planet from beneath it. It also would not be unprecedented in the existing lore as we already came across such a being before, Ultima. She was described as being parasite like and similar to Omega or Midgardsormr, originating from outside the star, either extraterrestrial or even extradimensional. However I do believe if this is the case then this threat will be saved for after 6.0 since that has long been stated as the end of the Hydalyn/Zodiark storyline and it wouldn't make sense to not focus on that and deal with some new threat then.

My best guess for 6.0 is that we go to Sharlyan as our hub city to see how to deal with the rising chaos and then go to Islabard for our exploration zones to put a stop to the tempering towers and Fandaniels and Zenos's threat. This leads to the final confrontation with Zodiark as Zenos tries to absorb him but hopefully fails and Hydalyn is dealt with in some way or another. However even though Zenos and Fandaniel are defeated, their efforts succeeded in rousing the parasite, maybe not fully awakening it so we have some time to build up the threat, and with Hydalyn and Zodiark now gone, it can begin to resume unimpeded as the Season 2 threat.