This is a theory on a potential outcome for Ephemer and the Dandelions if the Box theory isn't true, or if someone else doesn't free the Dandelions from the Datascape. It's also a 0.2 Fragmentary Passage-esque idea for an Ephemer game. ( A lot of the sleeping keyhole talk I learned from The Secret Reports on Youtube.)
Ephemer all alone (or with his Chirithy) in a ruined Daybreak Town reads the B.O.P to figure out what to do next.
Seeing what the future is supposed to have in store, attempts to figure out how to make it happen.
Ephemer unchained himself and Traverse Town appeared before him to grant him shelter after his world was destroyed.
Ephemer uses the Master Defender to reboot Daybreak Town into Scala 1.0
To rebuild a civilization, the only people Ephemer can think of are the trapped Dandelions, and the Player.
Upon Scala's founding, the Ark will be restored with all of the pods gone. That is except for the one that contained Ephemer which never left for the future. Ephemer uses this pod to transport himself into the sleeping Data-Daybreak Town.
If Scala 1.0 isn't rebooted yet:
Ephemer reads about Sleeping Keyholes in the Book of Prophecies.
He uses Traverse Town's sleeping keyhole to enter the Data-Daybreak Town (like Tron world in DDD).
There he sees all of the Spirits and either figures out they are the Dandelions, or his Chirithy informs him about Keyblade Wielders having the choice of sleeping as Spirits or living "another" life.
Ephemer's whole purpose for staying behind however was to rescue the Player from the dark fate the former had thrusted upon them (with no other choice of course).
From his perspective the darkness should have already spread throughout Game Central Station with the Player as a vessel.
However what Ephemer doesn't know is: The Player was pretending to be possessed, the Player had locked the pathway to GCS, and that the four Darknesses are trapped within the cable room connecting GCS and Data-Daybreak Town.
Ephemer is the only one left who is aware of the connection to GCS, so it stands to reason that he, being the one who opened the gate for the Player & Darkness, is the only one who can open the gate.
I think Ephemer is going to leave the spirits alone for a bit until he can figure out how to turn them back into humans.
Meanwhile, I think (possibly against his better judgement) Ephemer is going to open the gate to try and find the player, which will unintentionally free the four Darknesses back into Data-Daybreak Town.
With Darkness freed into Data-Daybreak Town, they will taint and spread through the Spirits, turning them into Nightmares.
Ephemer tries to defend himself from the Nightmares, but doesn't want to risk killing them like he almost did with the Player.
Ephemer gets cornered by three Nightmares and with no other choice, Ephemer once again has to fight his friends to survive.
Upon feeling bad for his hand in their demise, he notices they dropped dream fragments.
Chirithy tells him "Grab those fragments, it's the only way we can save them!"
Ephemer gathers the dream fragments and runs away before he's forced to fight against more Nightmares.
Ephemer uses Traverse Town's Sleeping Keyhole to return, and Chirithy explains to Ephemer how to use the dream fragments to reconstruct the Nightmares back into Spirits, just like Sora and Riku in DDD.
Ephemer reads more of the book.
Figures out that there will be future civilians of Scala 1.0.
Ephemer and Chirithy, use the dream pieces they collected from the fallen Nightmares to recreate the Spirits.
However many trips it may take, Ephemer returns to the datascape, to defeat the Nightmares one by one recreating Spirits with all of the dream pieces he collects.
However, there were four Nightmares left. These four Nightmares were the four lesser Darknesses, who confronted Ephemer, telling him the truth about how the Player was pretending to be possessed. They taunted him about how he betrayed his friend and is the reason they were able to kill the Player. Ephemer is saddened, and distracted by the thought of it all. The Darknesses seized his moment of weakness and attacked him with the intention of possessing Ephemer.
Either Luxu (who returned to Daybreak Town) or the Spirits protected him.
The four Darknesses assume the appearance of Player, Skuld, Brain and Lauriam.
Before their wills disappear they possess the Nightmares again fusing into the Nightmare Chirithy we as the Player fight before the Keyblade War.
Ephemer and the spirits defeated the Nightmare, as it dropped the last remaining Dream Fragments Ephemer needed to restore the last Spirits.
Ephemer leaves Data-Daybreak Town for the last time, and returns to Traverse Town. There, he reforms all of the remaining Dream Fragments into Spirits.
He looked inside of the book to find some hint to restoring the Dandelions back to their human form.
Ephemer somehow (POW) wakes the sleeping hearts of the Spirits.
This is how Ephemer restores the Spirits back into the Dandelions and how they become the residents of Scala ad Caelum 1.0.
Luxu's Possible Involvement
If Luxu returns to Scala 1.0 in an attempt to rescue the Dandelions, he either uses a corridor of darkness or uses the Sleeping Keyhole of Data-Daybreak Town to enter it.
Ephemer will be saved from the Nightmare Chirithy by Luxu, though I'm not sure whether or not Luxu will reveal his face to him yet.
Ephemer and Luxu return to Scala 1.0 by using the sleeping keyhole together.
Ephemer and Luxu restore the Dandelions back to normal and rebuild the the Ark using Ephemer's last pod that failed.
Luxu places Brain's heart in the Ark, leaves behind his hat and sends Brain to the future of Scala ad Caelum 1.0 to be remembered and reborn.
