My current headcanon is that this has nothing to do with Allag. Reading back through the
Patch Preview, it seems to suggest that Sophia already existed and was well established when Allag came to call. In fact, the entire civilisation that Allag encountered may very well be a
result of Sophia's existence and influence, her "
equilibrium" keeping the peace for an unknown amount of time already.
So, I think I'd heavily agree that the lyrics here are actually recalling the original summoning of the Eikon, likely during a time of internal struggle and maybe even civil war within the Meracydian nation. Albeit from the Goddess' perspective, I assume.
What's bothering me at the moment is the second part of the verse...
Her memory, fading fast,
Her mother sits, eyes downcast.
An eminent form in hand,
Farewells unsaid...
Looking at the Sophia we encounter, she does have an "
eminent form in hand", namely that ball, which I'm going to assume is "
Cintamani" (I'm justifying this based on the assumption that we're chanting, or "praying", to it during the course of the song - it's important). This makes me think that the Mother is actually someone important; She has possession of this ball, or I'm going to say
crystal (we'll come back to this), which has some level of notoriety or importance. She may even have been killed
because of it?
The third part then gives us some more detail of what happened next...
Now once a certainty, lost in grief.
A daughter's desperate cries, unheard pleas.
Forsaken ancient rite, on her knees.
A prayer passes from her lips,
Into her soul the Goddess whispers:
The Daughter is distraught, she's either witnessed or found her dead/dying Mother and is weeping on her knees. And in that desperate moment, she prays for her Mother to be returned to her. Her prayers are answered... (and she's enthralled in the process)
Here's the darkfoil hat part:
Why is there something of certainty about the Mother that's suddenly been lost? Why is she so important and why does she have Cintamani? My current guess, would be that Cintamani is a Crystal of Light. We've seen them before; Matoya has a very nice, spherical, one sat at home. And we know that they are extremely powerful... So powerful, in-fact, that they can out-perform our cheap-as Crystals of Light today, given that Hydaelyn had a lot more power back then (Inflation; go figure).
If that's the case, then was the Mother actually a Warrior of Light? A champion of her people who saved their realm from untold evils? And, in this multi-cultural Meracydian nation, did some have an axe to grind with their WoL? Did, perhaps, some of them fear or loathe her for her power? Enough to try and get rid of her?
We know from Unukalhai that WoL in other worlds have become god-like through their power and constant "winning", and depending on which side of that equation you fell on, there would conceivably be groups of people who wouldn't be appreciative of the effort and would see them as a menace.
There's also another comment in the 3.4 story, that one goal of the current Ascian antagonism aim to achieve something important: "when the beast tribes exhaust their belief in their primitive gods (primals), who will they look towards to save them?". 3.0 showed us a first glimpse of the Archbishop, on his last legs, questioning who we were and what we were becoming?
This brings me to a scary conclusion; Sophia is a fallen Warrior of Light. In fact, this could possibly explain Sephirot as well, as a Champion of his tree-like race. They are both Eikons, and through the prayers of their "followers" (for want of a better term) their Crystals of Light have reacted in the same way that any other crystals would given enough thought and prayer... they've summoned and empowered an idealistic, Eikonic version of their respective Warrior of Light, deiforming the real entity in the process. That's why Eikon's don't represent elements, they are the idealistic form of an actual Warrior of Light, blessed by the elements of the Crystals of Light that the Warrior obtained.
So the bigger question is; what happens to us if we keep winning???