1.
When Roxas leaves the Organisation, Axel tags along. He knows what his priorities are, now, and besides, he's sick of being bossed around.
Roxas isn't too keen on the idea – he's still angry and hurt, however strange that may seem – but Axel is stubborn and persuasive. He tries again to explain the choice he made, but Roxas doesn't want to hear it, and in the end it's practicality that seals the deal; together, they have a better chance of survival.
It pays off. Two against one, they thrash Riku. Even succumbing to the power of darkness isn't enough to save him. "Sora," he says just before he dies, and there are a million things in his voice. Roxas thinks he might even be able to name one or two.
They destroy Kingdom Hearts. Axel doesn't care – or, rather, he does – because his heart is right beside him.
Then, they run. They stay away from worlds they've visited before, but they still bump into the others from time to time. It doesn't matter, though. Axel still has no compunction about killing his former colleagues, and though Roxas is hesitant at first, he knows they have no choice. Pretty soon only Xemnas is left, and he is severely weakened.
Roxas forgives Axel when he forgets what he was so mad about.
Sora never wakes up.
Roxas doesn't care about the Heartless anymore, and so their numbers grow. With their vast Heartless army and no opposition of note, Maleficent and Pete conquer world after world. Eventually, Axel and Roxas have nowhere left to run.
2.
Axel's plan to turn Sora into a Heartless succeeds. He's rather more careful when securing Kairi, and when Sora finally arrives, he slits her throat in front of him. Rage and hatred swallow the Keyblade wielder's heart.
Unfortunately, Axel didn't really think his plan through. The Roxas from before was born of willing sacrifice, a gift from a pure heart. The Nobody which was created was an anomaly; barely a Nobody at all. That Roxas had no memories and no understanding of what it meant to be whole, but he could feel, and deeply enough for it to be contagious.
This Roxas comes into existence in the usual way, and is everything a Nobody should be. He remembers everything and feels nothing.
He returns to the Organisation with Axel's head as an apology, and is welcomed with open arms. After all, they need a Keyblade wielder.
Saix is displeased, still humiliated by his defeat at Roxas's hands and angry over Axel's betrayal. He sends Roxas on the most dangerous missions he can conceive of, but Roxas always comes back victorious.
About a month and a half after Roxas's return, Saix is attacked by lesser Nobodies gone rogue. The fact that they are Samurai is neither here nor there.
It is no great loss to the Organisation. He had already outlived his usefulness.
The day-to-day running of the Organisation is left to Xigbar, not that there's much left to run. Still, with Kingdom Hearts almost complete, all that means is fewer people to share power with. Every member of the Organisation thinks this, and yet none of them reach the inevitable conclusion. Not until it's too late for all but one.
Roxas surveys his kingdom and is… satisfied.
3.
Roxas refuses to let Axel die. He forces his way up through Sora's subconscious, dominates his mind, and breathes life into the man who taught him about friendship, the man he now understands that he loves.
Exhausted, he falls back into the dark recesses of Sora's brain. Now, though, he has carved himself a separate existence, and though Sora is in charge for now, Roxas is gathering his strength. He doesn't see why Sora has any more right to this body than Roxas himself.
Axel joins Sora, Donald and Goofy on their quest to rescue the fair princess and save the worlds, despite Donald's vocal (and not unwise) objections.
They defeat the remaining members of the Organisation. When DiZ's machine explodes, miracles happen; Roxas wakes in his own body, Sora next to him. While the others are distracted by Riku's return to his own form, Roxas and Axel disappear, leaving the heroism to those with hearts.
They aren't sure what happens after that, but the worlds seem safe enough and Xemnas never comes after them, so they assume he's gone, which implies in turn that Sora and crew are fine. They don't really care, though. They have their freedom and they have each other. Nothing else matters.
