RAMPANT speculation that's persisted since the beginning of the game.
First, we must establish that The Woken have a primal at all...
Ifrit
You avow yourselves blessed by gods, yet lack the capacity to
summon them to your aid. To which do you kneel, mortals?
Path Companion:
[Different for Each Race; to the effect of, "Our kind bows before no primal!"]
Ifrit:
Fools. Blind to the grace of those who would grant you protection
and bless you with their fortune. Your blindness is born of ignorance.
I smell the taint upon your soul. Is it Garuda...or Titan? Perchance...
Leviathan? ... The Paragon warned of the godless blessed. There
can only be one true god in this world, and those without cannot be
allowed to roam unchecked. Yet the Paragon has entreated that I spare
you, and so I shall─on one condition. Vow that you shall forsake the
summoning of Another. Do so, and your sins will be absolved. Refuse me,
and your soul will burn for eternity.
I think what Iffy is getting at here is that he knows for damn sure that our kind has a primal attached, that has, despite our rejection of it, blessed us with some kind of power. This puts the Amalj'aa in a tough spot - the Paragon (possibly one of the Archons referred to by a different name) taught them how to summon their Primals (aka eikon, meaing "icon," a symbol of esoteric religious worship), but demanded that The Woken be spared. Despite the primals being at war with one another, Ifrit agrees on the condition that we not summon our primal, whoever it may be. Thus, we do have a primal.
Also keep in mind that The Echo has only existence since Midgardsormr's apparent death, upon which the other primals were seen being birthed into the realm.
All the little references seem to add up...
When we first acquire the Echo, we hear a harp as she sings "Walk Free" [from the song Answers (more on that later)]. So us walkers of the path acquire the echo from a songstress. A songstress with a harp is the motif of the summon Siren, which is known for inflicting silence, which is cured by
echo herbs.
Siren's other main attack is called Hope Song... Sound a bit like Answers? "We must hope," "land of hope," etc.
Full Lyrics
I close my eyes, tell us why must we suffer
Release your hands for your will runs asunder
My legs long tired, tell us where must we wander
How can we carry on with redemption beyond us
To all of my children in whom life flows abundant
To all of my children to whom death hath passed his judgment
The soul yearns for honor and the flesh the hereafter
Look to those who've walked before to lead those who walk after
Shining is the land's light of justice
Ever flows the land's well of purpose
Walk free, walk free, walk free, believe,
The land's alive, so believe
Suffer (FEEL ME)
Lonely (FACE ME)
Weakness (TEACH ME)
Evil (FEAR ME)
Although ... one must ... stumble
Listen (SPEAK)
Although ... we might (TELL THEM), we must (TELL THEM) hope
Although we ... might (TELL THEM), we must (TELL THEM) , land of hope
Mother (HOPE)
Father (WISH)
Every ... wish ... has a ... home
We must go (ROAM)
Go (LISTEN)
Go (SUFFER) home (SANCTUM)
Swim ... leap...
And as (SPEAK) we (WANDER) sleep...
Sleep on... [ANSWER]
Now open your eyes while our plight is repeated
Still deaf to our cries lost in hope we lie defeated
Our souls have been torn and our bodies forsaken
Bearing sins of the past for our future is taken
War, born of strife these trials dissuade us not
Words without sound these lies betray our thoughts
Mired by your plague of doubt, the land she mourns
Judgment binds all we hold to a memory of scorn
Tell us why, given life, we are meant to die? Help us in our cries!
Witness
(We) suffer (we) borrow (we) reason
(We) follow (we) struggle (we) wander (we) listen
(We) whisper (we) shoulder (we) addle (we) weather
(Please) answer (you) answer (me) answer together
Thy life is a riddle to bear rapture and sorrow
To listen, to suffer, to entrust unto tomorrow
In one fleeting moment from the land doth life flow
Yet in one fleeting moment for anew it doth grow
In the same fleeting moment thou must live, die and know
I think we'll need a lot more info before we go about discussions of Primals and The Twelve, at this point. If I had to make a guess this early in the game about the nature of primals, The Empire's beef with them, the origin of Siren, and where this is all going? ....
I'd say that the primals have been crossing into our realm from the void for quite some time to feed off of the ceruleum in our realm. The Empire's strength relies on magitek powered by ceruleum as well... so basically, they see it as a clear good and evil situation - the ancient (primal) creatures, who come from the void and demand to be treated as gods and fed our resources, are evil, and the Empire, a society of this realm whose survival depends on resources taken by false gods, will act as the force of good. This would explain why they hate those who can use The Echo as badly as they hate, say, Ifrit. It's a power given by a false god in order to convince us to worship it (more on that later).
Ifrit says that only be one true god... but he refers to himself as a god, so I imagine that what he's saying is that only one primal can dominate our plane or they'll be at war. When the Empire invaded Eorzea to subdue us, expand the Empire, and take our ceruleum, they stumbled upon where our ceruleum was really going: into The One True God at the time; Midgardsormr. They managed to defeat it at such a terrible cost that their momentum was broken.
When Midgardsormr died, it created a power vacuum that every other primal and their mother seeks to fill at this point. They are present through the void to some degree, but need power to manifest here - and absolute power to dominate and monopolize our realm. To achieve these goals, they each pick a small domain or society to rule over and expand from there. Ifrit entreated with the Amals, Titan likened to the Kobold, Garuda found a home with the Ixal. Shiva took on the Northern Gigas territory, Leviathan figured his best chance was with the Sahagin... But when Siren came to the Woken... we failed to recognize her because we already have gods in The Twelve.
We've tried killing the primals before and they just keep coming back. Tales persist that the Lominsans successfully defeated Leviathan and Titan but that they were re-summoned later in no worse condition. Now, The Empire seems to know their true nature, and is invading to satisfy both fronts - take the ceruleum, destroy the primals, ALL of Eorzea's primitive races be damned.
I figure Gaius is the only one who knows that what's coming is much worse than expected. He's got a terrible feeling about Meteor... and I think I know why. I think the Allagan Empire successfully combated primals (hence why Gaius is after their technology, such as the runestones) and subdued The One God of their time - Odin. They imprisoned him and exiled him from our world for a lack of anything better to do with him... exiled him into space... where his jail cell would orbit our moon until we decided what to do with him.
And Nael Van Darnus just cast Meteor on it.
The Twelve, the true Gods of Eorzea, are sending the Archons back to deal with it. They're manipulating everything - they come to the beast tribes as Paragons, rally Eorzeans as Archons, antagonize The Empire... forcing everything towards one inevitable conclusion - the final battle for our realm with a force we've yet to even identify.