It seems you're thinking of these two things not only as separate stories, but also as happening at different times.
These stories intertwine and are part of one larger narrative.
Once again, spoilers ahead
NOTE: I used GamerEscape's Wiki to refresh myself on quests I did a long time ago.
Starting off
The initial few main scenario quests introduce game mechanics, special city-state functional NPCs, and unique story-line NPCs. This all leads up to our first encounter with "the Echo." Which leads to the first unified quest.
Level 18
Fade to White
We meet Melfina, learn more about our gift, become a Walker on the Path of the Twelve and select our Path Companion.
Level 22
Together We Stand
A main scenario quest, this is where we are fist introduced to the Imperial threat. Sylphs arrive at the Waking Sands and plea for help. The Empire has taken a specific interest in the Sylphs and are trying to destroy them and their podlings.
Melfina tasks you with aiding the Sylphs in protecting their podlings.
It's in this quest that we first hear mention of the Primals.
Grand Company introductions
The Empire rears its head on other fronts. To kick off our introduction into the Grand Companies, through a series of quests we learn that the Empire is planting roots around all three city-states and is actively trying to stifle their means to communicate and arm themselves.
We also see some familiar faces from earlier in the main scenario who recognize us as well as a shady figure seen around camps starting around the Easter event.
Level 25
Grand Companies continue
Another series of GC quests. This time they start with a brief quest then a speech by the GC leader attempting to unify their city-state as well as making a case for allowing adventurers into their ranks.
These quests move on to unique quests where Cid explains that the Empire has taken a special interest in Mor Dhona, and more specifically the area known as Silvertear Falls. Also, he explains his theory that the lesser moon Dalamund is having an affect on the flow of Aether -- especially around Silvertear Falls.
This series concludes with the player pledging allegiance to a sole Grand Company.
Imperial Devices
Also a Grand Company quest. Foul beasts have been gathering around a place known as The Thousand Maws of Toto-Rak in The Black Shroud. The player is tasked with investigating the occurrence.
Inside Toto-Rak, a Moogle gives the player several items, including a Magitek Cooling Plate and tells the player that Garleans have been investigating the area as well.
Level 30
Toll of the Warden
A main scenario quest, the Sylphs are in a tizzy again. The Amalj'aa and Ixali are at odds and are likely to summon their respective Primals. It's up to the player -- or as the Sylphs say, the Woken ones -- to use their gift and speak to the Beats tribes lest they unleash a devastating power.
With the recent emergence of these Primals, the beast tribes have become unwilling to trade crystals with the five races as they have in the past.
Negotiations end abruptly due to the emergence of a creature known as the Ascian.
It Kills with Fire
We've been tasked with vanquishing the primal known as Ifrit!
First we must meet with an Elezen by the name of Louisoix from a group known as the Circle of Knowing. As a throw back to Cid's explaination that all is not well with the flow of the Aether, Louisoix explains that to exist in our realm, the primals draw on the Aether.
As such, they must be defeated before they drain the crystals completely. Otherwise the world will become a wasteland.
Louisoix sends you on a brief quest and through your efforts is able to create an item that will allow you access to Ifrit's sanctuary, the Bowl of Embers.
Upon achieving victory over the primal, the player is greeted by Legatus Nael van Darnus of the Vilth Imperial Legion. He gives a message mentioning the "Crimson Star," -- which, in theory, is the red moon Dalamund Cid spoke of earlier.
Upon returning to Louisoix, the player learns that not only did they not best Ifrit permanently, but the attack by the Imperial likely fed the Lord of Inferno enough Aetheryical power to significantly enhance his strength.
Level 34
Forever Taken
Back to the main scenario, it is believed you can bribe the Ixali into reopening the lines of trade.
The Sylphs have requested that the player gather unaspected crystal. The player travels to Silvertear Falls and buries crystals in the soil there. After a short time, the player obtains the now unaspected crystals.
Meanwhile, the Path of the Twelve obtained a linkpearl the Empire has been using to spread propaganda, stating that the beast tribes intend to use the "eikons" (derogative for Primals). The Sylphs explain that it was a being know as the Paragon who taught the beastmen to summon the Primals from the Aether.
Level 38
Lord Errant
The player and their path companion set out on their own, the Path Companion certain they can reason with the beast tribes.
Things, naturally, don't go as planned and the player is again face-to-face with the Lord of the Inferno.
Ifrit eventually speaks to the player. Albeit cryptically, Ifrit does mention that the Paragon told him that the "godless blessed" should be spared. Hinting at why the player and company were able to overcome the Primal in the GC quest, but why he also saved them from the Legatus' attack.
Level 42
Of Men they Sing
A brief mission, the player and their Path Companion save several Ala Mihgan resistance fighters from an Imperial Assault in the Black Shroud.
Level 45
The player is tasked by the Grand Company to investigate the Dzemael Darkhold and to discover why the Empire has chosen this as their base.
You discover a Magitek Dousing rod, which can be used to track down crystals. It is believed that the Empire is searching for Crystalized Aether to aid in summoning a primal.
Level 46
Futures Perfect
The Ala Mihgan resistance members you saved have spoken with Melfina. They want to steal an Imperial Airship.
Your strong-headed Path Companion and the Resistance members have rushed off to, where else, Silvertear Falls in Mor Dhona to attempt to commandeer an Imperial ship despite the warnings made by Melfina of failed past attempts.
After an encounter with Imperial soldiers, you find that the Resistance has been slain by a lone member of the Empire, The Black Wolf Gaius van Baelsar Legatus of the XIVth Legion.
Your friends from early on in the main scenario and GC quests show up to defend you against the power of the Legatus. However, the Legatus shows off the awesome power of the Empire and makes short work of everyone.
The last thing we know of the story is our friend from our very first few steps in Eorzea that we are not yet ready to fight the Empire.
Conclusion
The Grand Company quests and the Seventh Umbral Era events are filling in story so that all story content now can drive toward the cataclysm that creates 2.0.
As can be seen in the above listing, while the SUE events just now are being added, they're intended to have taken place in tandem with the main scenario events. Both quest lines revolve around the Empire's interest in the Aetherial power around Silvertear Falls and their desire to control the power of the primals while attempting to convince the people of Eorzea that the primals are evil and should be destroyed.
I believe as we move forward, new quests will take off from Futures Perfect.
There still are many loose threads. What is the Paragon? What is the Ascian? How close is the Empire to summoning a primal, and how can they actually do it? What is the truth to the primals -- are they good or bad? Do primals really drain the Aether or is this more Garlean propoganda -- thus covering for their own misdoings?
To the original point, it is quite obvious that SE has crafted the SUE events to use the main scenario as part of what has been going on.
I think moving forward we'll see these move into one storyline, which will make more sense that when 2.0 comes, all the quests will be wiped.
As I said before, the story still will be there, but to new players these will just be backstory. As for how characters interact with us in 2.0, I'm sure SE will come up with something. Despite all their recent faults, one thing SE seems to never get wrong is continuity.
Also:
There is no meteor.Ifrit, and ALL the primals, will still be alive and a part of the story after the fall of Meteor.



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