- Because the light of the Fifth Mothercrystal had been drained, Al'taieu was falling into another dimension. Correct me if I'm wrong, but the five red lights and portal-looking thing above the Palace of Hu'xzoi is the portal to the aforementioned dimension looming to open over Al'taieu, and it is appearing in the sky because the space containing Al'taieu is coming in contact with/falling into this other dimension. That red dimensional portal majiger is the exact same color/shape (but larger) of the phenomenon that appeared over Port Jeuno as a result of Abyssea coming dangerously close to Vana'diel. And, keep in mind that Abyssea is another dimension.
- So far, Abyssea only takes place in areas with mothercrystals; namely, the three crags.
- In the CoP plotline, you take away some of the light of each mothercrystal when you do the promyvion of that area. The intention of this was to imbue you with the lights of the other four crystals, then "break you open" before the weakened fifth mothercrystal. Kind of like a quadruple bypass surgery. However, if you take the light from the other mothercrystals, which were already infected with Emptiness, that means you are weakening them. As we see with Al'taieu, if you weaken the light of a Mothercrystal too much, the region surrounding it falls into another dimension. And all the visible effects of this "other dimension" as seen through the portal over Hu'xzoi look strikingly similar to the known "other dimension" that is Abyssea.
- So, my theory is that portals to Abyssea are showing up in the three zones with crags because the mothercrystal at each crag has been weakened, and is drawing our dimension/world threateningly close to Abyssea, this alternate dimension. This also implies that Scars of Abyssea will introduce Abyssea-Vahzl (Abyssea-Xarcabard?), and Heroes of Abyssea will introduce Abyssea-Al'taieu.
This still doesn't explain why Cavernous Maws link the two realms. Could just say that a moogle did it. Or, in this case, a moogle made Atomos do it.
Or, I could be completely wrong about all of this. It's no more than just a bunch of ideas that swarmed my head at once after watching the cutscenes after unlocking Sea.