What I got from the U.X. ending
Ephemer was devastated by the player's fall to darkness and betrayal.
Ephemer got into one of the last two pods alongside Skuld.
Ephemer's pod failed (?) He is left as the sole survivor in a destroyed Daybreak Town.
(Theory) Ephemer most likely read the Book of Prophecies and learned the truth about everything that was supposed to happen and everything that will happen in the future.
Using this knowledge and Foresight, similar to Aqua's restoration of Land of Departure, he reboots Daybreak Town into what appears to be a Goth-like Scala ad Caelum.
Being the first new keyblade master, Ephemer would possess the ability to transfer his heart to the body of another.
Brain sends Ventus, Lauriam and Elrena to different Worldlines.
Attempting to figure out how to rescue his friends from the datascape, he is confronted by Luxu for the first time.
Luxu and Brain switched hearts or bodies.
Brain got in the pod to hopefully meet up with Ven, Lauriam and Elrena. Luxu somehow escapes the Calamity of Daybreak Town.
Luxu bestows the The Master's No Name keyblade onto Brain. Brain takes on Luxu's role and Luxu no longer possessing the means to escape, gets in the pod and arrives in Scala ad Caelum.
* I believe the scene with Luxu in the desert is the same cutscene from the beginning and end of Back Cover. When Chirithy is role calling the Foretellers, Luxu's scene is the first half of the Union-X counterpart. He's dragging the Box with his left hand, while holding the No Name keyblade backhand in his right hand.
After he stops, he glances down at the keyblade, places his hand over his heart and reiterates the famous KH quote, "May my heart be my guiding key."
The big difference here is that the Union-X counterpart shows us Luxu removing his hood and revealing his face which resembles that of Brain.
As for what this means, that's still difficult to tell. If this scene does predate the Keyblade War, that would mean that Luxu always had the face of brain. That would also mean Nomura had at least Luxu's Union-X fate planned out since Back Cover. The problem is that these scenes can still take place after the fall of Daybreak Town, implying Luxu took Brain's body or Brain took over Luxu's role.
I think the hearts of Brain and Luxu both reside inside of Brain's body that awoke in Scala ad Caelum.
I think Luxu bequeathed the No Name keyblade onto Brain. However because of this, I don't know how he could leave Daybreak Town on his own without using the Ark. Also, the Master tasked him with watching over the Keyblade, meaning he would have to be around the current wielder or at least in the same area. If this theory is true, then every criteria would be met.
Luxu and Brain share the same goal of rescuing the Dandelions and escaping Daybreak Town. Luxu bequeathed Brain. Just like Eraqus resided within Terra's heart by the end of BBS, I think Luxu will choose to reside within Brain's heart, as they take the pod to arrive in a future Scala ad Caelum. This way he can watch over Brain and his Keyblade, as well as recording relevant information with the Master's eye.
Also No Name ends up mounted on a crest in the present day Scala ad Caelum.
An important thing to note is that the Brain who wakes up in Scala and the Luxu with Brain's face both lack his signature hat. I think when Luxu and Brain did their body shenanigans, the hat was left behind in the ruined Daybreak Town, whether or not it was on purpose, I don't know. But if Brain got in the incomplete Ark, then his body would disintegrate. He would need someone with memories of him and a medium to recreate his body. I think Ephemer, upon waking up and rebooting Scala ad Caelum, found and kept Brain's hat as a keepsake. When Sigurd meets Brain he "returns" Brain's hat. Ephemer had the memories of Brain, and his hat acted as the medium to recreate Brain's body.
(An Alternative) Even if the Brain that wakes up in Scala was Luxu, the fact that No Name ends up mounted in one of the classrooms means that the wandering Brain eventually made it to Scala ad Caelum. Maybe with Brain's memories and Luxu's jacket, he was the reason that Luxu was recreated in Scala ad Caelum.
After almost being killed by the Player, Ephemer carried Skuld (like a princess) to the Ark as they left Data-Daybreak Town together.
Skuld and Ephemer get in the last two pods after seeing their home on the edge of oblivion.
Ephemer's pod failed to leave, but Skuld successfully traveled to the future.
It wasn't shown, but we know from KH3 that Skuld arrived in Radiant Garden around the time Xehanort is taken in by Ansem the Wise.
She is (all but freaking confirmed at this point) the "Subject X" referred to in the Secret Reports.
However, eventually Ansem the Wise and Luxu released her from captivity.
Her fate afterwards is unknown.
Fate of Ventus, Lauriam & Elrena
Ventus, still harboring a "Darkness" inside of him, Lauriam and Elrena are all sent to the future as they are scattered across different worlds in different times.
Lauriam arrived in a field of flowers in what was most likely "Dwarf Woodland".
Elrena arrived on a craggy Cliffside during a thunderstorm in what looked to be Enchanted Dominion.
Ventus arrived in a desert area, that was the Keyblade Graveyard, but with no Keyblades in sight. He was being approached by what was most likely Xehanort.
The player seemed to be possessed by the Darkness that resided within them and attacked Ephemer and Skuld.
As they were going to kill Skuld, Ephemer keybeams them into Unreality.
The Player tricked Darkness, locking themselves with the other four "Darknesses" in between Data-Daybreak Town and GSC. This way Darkness was confined and unable to spread it's essence throughout the game worlds.
The player is killed by the Darknesses, and instead of choosing to become a spirit with Chirithy, chooses to live "Another" life, being reincarnated as the main antagonist, Xehanort.
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