I'm not entirely sure how the story would play out here, especially in regards to the Corvosi faction, but I'm thinking there would probably be a major twist in that one of the remaining Ascians wholly against Fandaniel's attempts to recreate the Final Days would be actively helping the people of Corvos resist the influence of the tower there. This Ascian would reach out to the WoL and the Scions, promising a way to meet the leader of the Legion within Corvos.
While the WoL and the Scions are expecting an ambush, they instead learn that she witnessed Emperor Varis being assassinated, and quickly grabbed his soul as a potential backup plan. Only after she learns of Elidibus being defeated on the First, Garlemald's descent into chaos, and Fandaniel's completely unhinged plans does she get the idea of trying to take matters into her own hands. She had grabbed a clone body of Emperor Varis and restored him back to life within Corvos in the the hopes of having him calm the chaos within Corvos. This, she did, right before the Grand Company of Eorzea arrives. (And I say this Ascian is female because there are no female Ascians that have played a major role in the story thus far, Igeyorhm wasn't any different from the mook Ascians we saw very early in the plot and extremely underdeveloped at best.)
Of course, NOBODY would be pleased about this, least of all Varis himself learning of how Zenos has basically screwed everything up, his original body now being host to an Eikon that tempered and destroyed most of Garlemald and is now an active threat to the entire world, how he was saved by an Ascian, and that his Empire is now at the mercy of everyone else. He refuses to accept the idea of asking the Eorzeans for help, and is about to order the entire Legion to ambush the WoL and the Scions until a messenger reports news of Gaius arriving with several members of the XIVth and VIth Legions in an attempt to parley with the Corvosi Legion on behalf of the Grand Company of Eorzea. The former Emperor is clearly glad to hear that Gaius had survived the events after his so-called assassination, and requests for Gaius to arrive in person and explain how Eorzea has treated his people before deciding on any further action.
This isn't exactly a happy reunion. Gaius calls him out for even considering using the Black Rose and the Weapon project, and is quick to point out that Varis himself along with all of the other surviving Legions are now basically exiles with a destroyed homeland as well. Alphinaud also makes it abundantly clear that they won't be marching to rescue Garlemald just to restore Varis back to the throne - that the fate of Garlemald as a nation is but only one part of determining the fate of the world, a callback to how Varis once told Alphinaud and the WoL that the fate of Eorzea mattered little compared to that of the entire world when they first met back in Heavensward.
With that, Varis decides to challenge the WoL, the Scions, and the 'Grand Company's strongest warriors' to a battle to see if they truly have what it takes to march on Garlemald and defeat Zenos, marking the first trial of the expansion. He makes it clear that if the group is unable to best him, then the Legion will resume attempting to retake Corvos and carve out a new nation here, rather than risk everything on an alliance doomed to fall against Zenos.
Of course, the WoL wins, and the Legion declares that they will secede control of Corvos to the Corvosi while they focus on their imminent plans to assault and retake Garlemald. But first, they have to deal with the tower in Corvos. After that, the topic of exactly how Regula met his end comes up, along with some other Imperials on the side talking about the Emperor's friendship with someone that was supposed to be a commoner. It is then that everyone learns that Emperor Varis was completely unaware of Regula's sacrifice. He had been told that Regula had been slain by the WoL and the Scions, and everyone finds out that Regula's body along with the Imperial soldiers that were supposed to be sending him back had never made it to Garlemald. He doesn't believe the WoL's account of events at first, until the VIth Legion soldiers that are present vouch for them. They then get the idea of finding some way to make the Graiton worthy of flight once more, to see if it has the firepower to destroy all of the remaining towers that may be locking down all of the other Legions elsewhere.
As for the rest... I haven't thought that far ahead, namely what happens between Corvos and Garlemald (since there would probably have to be at least two more zones). Maybe Fandaniel learns that Varis is alive (or he knew that was always a potential factor since he would have seen the other Ascian escaping with his soul), and decides to do something with Regula's body to really screw with him. There's also the topic of Titus and the 3rd Legion, not sure how that would be changed.
Events within Garlemald itself might play out mostly the same. Varis would be out of the way piloting the Graiton to destroy all the other towers and coordinate the remaining Legions' march on Garlemald from the air, while Gaius establishes contact with said Legions on the ground. Quintus wouldn't get the memo on what's happening because the Tower of Babil would be cutting off all communications at that point, and would likely be immensely shocked at the idea of Varis actually cooperating with the Grand Company of Eorzea, even going as far as to believe that this is some Eorzean trick and that this Varis is an impostor - after all, Quintus would probably be the type of person to believe that the true Varis would not have been hiding in Corvos while his people were suffering in Garlemald. His suicide would still happen before anyone gets a chance to talk him out of it.
Varis would probably arrive soon after with the Graiton, only for the tower to fire off that massive tempering pulse. The WoL would get taken during the chaos as before, but Varis ALSO gets taken (or the WoL witnesses Varis being taken and attempts to give chase, only to arrive right as Zenos defeats him and the WoL also gets knocked out by Fandaniel while distracted on the side). Things play out the same as before, with Varis' fate unknown. So after the WoL regains control of their body, the rest of the Garleans arrive and join in the assault on the Tower of Babil in the hopes that they can rescue Varis.
Of course, Varis is actually dead for real this time, the WoL and other leaders of the assault group would arrive to find out that he's been used to power up Anima. Anima would be converted to becoming the second trial boss for the expansion. The rest of the expansion plays as it did before, with the moon being the final zone, up until Zodiark is defeated.
The story would end on a cliffhanger with the threat of the Final Days looming overhead, with everything involving the Loporrits being coming into play during the post-expansion story, along with signs of the Final Days gradually breaking out across the Three Great Continents. The entire world would be forced to unite against the impending threat over the patch cycle, pitching in on research about how the Final Days worked, rather than it being something that only the Scions, the Loporrits, and the Sharlayans really knew about. Maybe the world would learn of the concept of Dynamis, and figure out that the Garleans would be especially vulnerable to the Final Days phenomenon given all that had happened to them - but maybe they could potentially wield Dynamis more easily too. The seemingly friendly Ascian herself would likely transform into a Blasphemy when asked about the Final Days, accidentally triggering the memory of her past life and pushing her over the edge.
The next expansion involving Elpis and Meteion would likely begin in a different region on the Three Great Continents getting hit really hard by the phenomenon. I honestly haven't thought about this part at all, but I've read plenty about how people would have wanted the Elpis arc to be much more fleshed out than it was.