The protagonist is dead; Brain is missing, and Ephemer, Skuld, Lauriam, Elrena, and Ventus have made it into the future. Regarding the protagonist, they sacrificed themselves to trap four of the original 13 Darknesses in the collapse of the data world, allowing Ephemer and Skuld a chance to live on in the future. Meanwhile, Brain had an unresolved encounter with Luxu after sending Lauriam, Elrena, and Ventus on their way. While the protagonist reincarnated as Xehanort, the fates of the other characters remain a mystery.
Quest 979 is the final quest in the Kingdom Hearts Union Cross storyline, and its cutscenes "Destinations" and "An Unfamiliar Town" unveil what happens to most of the other mentioned characters. While some of their fates are fairly straightforward, others are more open-ended. This writing is the fourth and final entry in a series covering quest 979, and it interprets the events of the mentioned cutscenes to clarify the Kingdom Hearts Union Cross finale.
Destinations
Ephemer's lifeboat returns to Daybreak Town sometime after its destruction. The dark storm didn't finish destroying and dragging the planet into darkness. As such, after making it to the future — if he time traveled at all — Ephemer's pod cruises Daybreak Town's debris-filled waters. When a piece of debris chocks the pod, it opens, and a silhouette of Ephemer emerges from it.
Maleficent, of course, lands at the beginning of Kingdom Hearts 2. Diablo, her raven, carries her cloak from Hollow Bastion to the Mysterious Tower, where Flora, Fauna, and Merryweather will inevitably stumble onto it, suffer her memory, and inadvertently give her back her body. After which, she'll go on to perform all of her KH2 shenanigans.
Lauriam and Elrena obviously land in the same time period. When exactly remains a mystery, but it's likely just before the events of Kingdom Hearts Birth by Sleep — same as Ventus. While the two are in the same period, however, they land in different worlds. Lauriam wakes up in a meadow in Dwarf Woodlands, while Elrena lies knocked out in the middle of a storm in the Forbidden Mountains of Enchanted Dominion. Neither of them has their pods, and they also still have their bodies.
Still out cold from his tussle with Darkness in quest 977, Ventus lies in the middle of the Badlands. Like Lauriam and Elrena, he still has his body, but his pod is nowhere in sight. Unlike them, however, he is approached by a silhouette, one that — while admittedly nondescript — likely belongs to Master Xehanort given the events of Kingdom Hearts Birth by Sleep.
Then there's Luxu, who, of course, doesn't travel into the future but instead lives out his lifetime, as well as multiple others', filling out the Book the Prophecies. His last appearance in Kingdom Hearts Union Cross sees him dragging the Master's box across the Badlands, reciting to himself the Master's motto, "May my heart be my guiding key," which takes on new meaning since he's the traitor the Book talks about. The cutscene also sees him revealing his face, which is when things get weird.
Luxu is wearing Brain's face, and there's no context why — actually, there is, but it doesn't match up with this scene. In the Kingdom Hearts 3 Secret Reports — specifically, report 11 — Luxu claims that he bequeathed the Gazing Eye Keyblade to one of the five new Union leaders and then watched them head into the future as directed by the Master of Masters. Quest 979's cutscene "I'll Figure it Out" implies that this leader was Brain, as does this current scene.
However, Luxu also states in the report that he goes on to be "Keybladeless," jumping from body to body and simply watching as the Eye gets passed down from one wielder to the next. Hence why he states at the end of Kingdom Hearts 3 that the Keyblade finally returned to where it belonged: his hands. Simply put, with all things considered, Luxu shouldn't be in Brain's body, especially since his body was still in working order. Yet it doesn't make sense for this to Brain either because of this next scene:
An Unfamiliar Town
Pod-less, Brain wakes up in the streets of Scala Ad Caelum sometime in the future, where a shrouded man named Sigurd approaches him and hands him his hate. He then makes Brain wait a moment while he reports his arrival to headquarters. Once he phones that in, he grants Brain an explanation as to what's going on: Brain somehow escaped Daybreak Town's destruction, and it was decided that he would arrive at this moment in this time period where Sigurd would greet him.
Sigurd plans to give Brain a more detailed explanation at headquarters, but before he can lead him there, he finds himself having to answer Brain's desperate questions regarding the whereabouts of his fellow time travelers. According to Sigurd, Brain is the only individual who landed in the current time period. While Brain's disappointed by that, Sigurd, again, promises to clear up everything once they make it to headquarters and proceeds to lead the Union leader in that direction.
On the way, Brain sees something unexpected but welcome: a monument to Ephemer, who Sigurd claims is the founder of Scala Ad Caelum and the very first Keyblade Master. Brain takes pride in Ephemer's status as he considers him his best friend and because it means Ephemer managed to fulfill Ava's request of keeping light alive despite them all failing to keep the Dandelions safe. He knows that they succeeded, and with that, Kingdom Hearts Union Cross comes to a close.
Ephemer and the Two Brains
Here's a possible explanation for these characters: Ephemer doesn't travel into the future. His pod fails to launch, as hinted at in "Ephemer and Skuld" which doesn't show the pod's travel animation before the tower collapses on it. However, despite not launching into the future, Ephemer isn't sucked into the dark storm, and so, after it passes, he finds himself among the debris of Daybreak Town. It makes sense for Ephemer to have failed traveling into the future because he's the only character to emerge from a pod.
Once Ephemer leaves his pod, he reads the Book of Prophecies, finds Brain's hat, builds Scala on top of Daybreak Town, teaches his apprentices about his fellow leaders — which gives them memories of Brain — and then he gives Sigurd Brain's hat as well as the coordinates to find his heart, fulfilling the conditions for Brain to wake up in Scala with his body.
There weren't enough pods available for everyone — the protagonist, Brain, Ephemer, and Skuld — to all make it into the future. After Brain impressed Luxu with his resolve to stay behind and die to give the others a chance, Luxu decided to save his life. Having read the Book, Luxu knows Brain makes it into the future, so he casts aside his body earlier than expected, takes over Brain's, and then thrusts Brain's heart into the future using whatever method the Master used to make it without using a lifeboat.
In this case, there are two Brains: Luxu, who's piloting Brain's original body, and Brain himself, who received a new body upon making it into the future. It's no different from how Sora and Roxas could physically co-exist despite the latter using Sora's body. Essentially, Luxu hasn't passed on the Gazing Eye Keyblade yet, which explains why he has it despite body-hoping. He only escaped Daybreak Town in Brain's body via a Dark Corridor, and then he likely returned to help Ephemer build Scala or, at least, watch him build Scala. He then passed the weapon onto one of Ephemer's apprentices or Ephemer himself.
Subject X
Kingdom Hearts Union Cross' finale doesn't cover what happens to Skuld following Daybreak Town's collapse, but she likely landed in Hollow Bastion sometime after Kingdom Hearts Birth by Sleep; it's likely she's Subject X, the mysterious time-displaced girl that Apprentice Xehanort experimented on in an attempt to restore her lost memories — the same time-displaced girl that Lea and Isa promised to help break out, and the same girl that claims her strongest memories are of "four friends and a key."
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