In the Epilogue, Casra II said that an Anti-Photon political movement may start up within the civilian sectors of Oracle in the future and Shiva told the Guardians that even if they managed to pull through all of this, they will just end up the victims of a society that fears them. I think this was foreshadowing the back story of the Meteorn. Like after all of the universe-ending chicanery going on, civilians are just done with Photon superweapons and they elect to seal super powerful ARKS like the Guardian in a dimensional stasis to prevent anything like the Profound Darkness from ever coming again.
Fast forward 1,000 years on the surface of Halphas. Photon technology has been deliberately stalled so the only significant advances made were miniaturization of Dash Panels and other conveniences. ARKS has completely or near-completely divorced from the guidance of Akashic beings like Xion, Xiao, and Xierra. The events surrounding the Guardian, the Falspawn, Dark Falz, and the Profound Darkness have been shrouded by time from the memory of the general populace. The emergence of the Meteorn relates to the existence of the DOLLS: either the DOLLS were part of the system meant to keep the Photonic Superweapons sealed that went haywire as the seal decayed, or they are a threat that emerged from elsewhere in the universe and the Meteorn were released as a fail safe to deal such an occurrence. The side effect of long-term dimensional stasis is the loss of memories relating to personal history.
As we land on Halphas we will meet a new cast of characters that are hopefully very interesting and very stylish that people can draw and fangasm all over like how the Genshin Impact playerbase does because it's good for marketing the game and SEGA should probably try to do that if they don't have better characters planned with better characterization and more story to them. We will encounter the new ARKs that might have been founded by someone we knew in the past.
I believe that as we move deeper into the story, we will eventually recover more of our memories as we uncover more of the past. However, after we beat one or two minor antagonists we will eventually find ourselves facing off against another protagonist that we cannot beat with photons which triggers the full recovery of all our memories. We will remember what went on during that revolution along with what happened to all our friends and allies. Filled with fury and anger the Guardian becomes the new Profound Darkness and uses it to overthrow the new antagonists that's part of the larger faction that reduced ARKs to it's current state. We might learn that this new faction was what ARKs once was until the revolution overthrew it and killed some of our friends in the process during the war which could have led to the Profound Darkness awakening in the Guardian which then forced both sides to unite and seal away the Guardian.
We will eventually face off against this new cast of enemies from this new organization that used to be ARKs, who aren't good guys or bad guys but simply those who are fighting against you because you are the Profound Darkness now after all. You might kill some of them or you might befriend them. Then finally it is revealed that the one who is running this new large faction of the enemy is a new entity like Xion or Xiao who awakened in the Mothership after we moved Xiao to Amduskia. But before we can get to them we have to defeat Xiao, who became corrupted by Amduskia. There's a certain region in Amduskia that has been badly corrupted by the Profound Darkness' influences in the past. This ominous area is filled to the brim with overgrown minerals and traps in the form of crystal barriers. The former vanguards of the Draconians that reside here have also been twisted beyond saving, even among the higher ranks. The original consciousness of the fiery half of Amduskia lays dormant here. Later, Xiao would complete the consciousness' lack of intelligence and become the second protector of the planet.
Once we go through that mess, that's when the Profound Darkness truly frees itself from us to try and spread it's influence over Xiao who's most vulnerable in his current state which forces us to end the last Akashic being apart from Xierra. Then the main enemy becomes Dark Falz again with some previous antagonists gaining it's power which causes a whole new conflict to arise and then ARKs builds a new space-faring fleet and we fly across the universe once again to see the fate of the universe that we've left it in over the past 1000 years with new and old planets alike.