Luxu used one of the lifeboats to ship "the true dandelion" off into the future, believing it's what the Master of Masters wanted. Who he spirited away remains a mystery, but they wore the same white cloak as Ventus during his first appearance in Birth by Sleep. Regardless, with Maleficent having taken one lifeboat already, Luxu's actions have left only five pods for the rest of the Dandelions, and that's not nearly enough.
"The Shadow's Identity" and "Resolution" cutscenes of Kingdom Hearts Union Cross quest 978 reveal just how many other bodies or "shadows" Darkness has. They also see the Dandelions decide who among them will take the lifeboats back to the real world. The quest is the second of the last three in the Kingdom Hearts Union Cross storyline, and it's the first of the game's two-part finale. This writing interprets and recaps its events to clarify the Union Cross story.
The Shadow's Identity
Luxu and Darkness don't understand each other. Luxu can't understand why Darkness didn't fully read the Book of Prophecies when it had the opportunity, instead opting to only read the parts detailing its goal of spreading. If it read the full Book, it wouldn't have to ask him who'll end up using the last five pods. As for Darkness, it can't understand why the Master trained the Dandelions only to abandon them in the data world. Nor does it understand why Luxu would follow him when he doesn't know either.
The only common ground the two can find is their mutual dislike. Luxu may not know the Master's intentions, but he can at least guess at them, and while he may not be certain of those guesses, he is certain of the Master's aversion for Darkness, and that's all he needs to know. Darkness can relate to this because it's not fond of the light either.
Since Darkness is so interested in the Master's plans, Luxu wonders what it's scheming to challenge light, so Darkness indulges him. It plans to use Data Daybreak Town's connection to the other data worlds to spread to them and take over. It will also use Ven, its chosen one, to make its way into the future and take over everything there, too.
Luxu does not like that answer at all. The idea of having to live with Darkness no matter what world or timeline he's in is unacceptable. The thought actually leads him to pull his Keyblade, an action that leaves Darkness pleasantly surprised. It was under the impression that Luxu couldn't interfere, so Luxu clarifies that the Master told him not to help the Dandelions, and he isn't. He's fighting for himself, which Darkness finds strange because Luxu knows he can't destroy it.
But destruction isn't Luxu's goal. He knows that the longer Darkness exists without a tangible form, the more it loses its ability to act autonomously. It had a body when the Master was a kid but abandoned it to defeat light. Then it realized it couldn't maintain its will without it, which is why it's going around stealing bodies with hearts. It may think its plan to spread is grandiose, but Luxu finds it pathetic, so he's going to delay it.
The insult triggers Darkness into attacking Luxu, but he teleports out of the way and continues: He knows that there are five other Darknesses, or "shadows," aside from itself and that the Dandelions are fighting one in the data world, so he wants to know the whereabouts of the other four. Never one to turn down questions, Darkness compliments Luxu's knowledge and tells him that the other four are in the data world as well. With that, both parties understand that there are no other shadows or masters to get in their way, so their battle begins.
Resolutions
Upon entering the tarnished basement, the Dandelions discover only five pods left for their seven people. So they make their way to the room's terminal to see if they can learn anything to inform their next move. However, the terminal shows them that outside the tower, a glitch storm is tearing Data Daybreak Town apart with cyclones, and it becomes apparent that the group no longer has any time left to deliberate; they need to choose their five survivors now.
Skuld and the protagonist ask about the other Dandelions, and Brain reminds them they'll be put to sleep, like a computer in sleep mode. It's what Ava told them would happen. Essentially, should the data world fall to darkness, it and its inhabitants won't be destoyed, more like put into stasis. With Ava's statement in mind, Brain suspects this is why the Master chose this world to keep them safe during the Keyblade War. Simply put, they all need to worry about the end of the real world, not the digital one.
However, the group weighs the risks of using the lifeboats. Brain recognizes that they have no idea where the lifeboats in the real world will take them, but they'll have to use them when they get there. When Lauriam points out that both staying and going have their risks, Brain realizes that if no one returns to the real world, then no one will know that the data world needs to be rebooted. All the Dandelions will be as good as dead, which would defeat the whole purpose of them surviving the Keyblade War.
So the decision is made: they'll return. Being first- and second-in-command, Ephemer and Brain feel they should split up, so Ephemer assigns Brain to the real-world team, believing he'll be the best shot they all have at surviving. Skuld then takes the liberty to assign the protagonist, Elrena, and Ven, the non-Union leaders, to Brain's team as well. She then insists on Lauriam taking the final pod, as the real world holds the best chance of him reuniting with his sister — if such a thing is possible.
Skuld's selflessness leaves Lauriam speechless. He only finds his voice again when Elrena protests taking a pod, believing she doesn't deserve one because she's not a Union leader. Lauriam convinces her otherwise by reminding her that she's the reason he's gotten this far in his search for Strelitzia and by asking her to help him finish the job. Brain chimes in, too, promising that he'll find a way to save everyone, so no one should worry about the limited seating.
With that, Ephemer asks one last time who's returning to the real world, and the protagonist forgoes their seat. They aren't a Dandelion, and they're only here to support Ephemer as his friend, so if he's staying, they'll stay behind with him. Being a part of the trio, Skuld decides to remain behind with them, too, which Brain thinks is fine. He already has an idea on how to save all of them, so leaving one pod behind could be a good thing.
This settles it. Brain opens the pods, and at Ephemer's request, Lauriam agrees to look after the still unconscious Ven. Before Brain enters his pod, he promises Ephemer that he'll take care of everyone, then he hands him both the Book of Prophecies and, surprisingly, the Master's Defender. Both apparently belong to Ephemer, and Brain thinks Ava trusted him with the items knowing he would hand them over if the time came. Brain never needed to resort to the Book, but he encourages Ephemer if the need arises. He knows Ephemer's always wanted to read it anyway.
With one final goodbye, Ephemer gives Lauriam, Ven, Brain, and Elrena his best wishes before sending them all off to the real world.
Kingdom Hearts Union Cross is on IOS and Android.