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One of the last bosses is young Xehanort. After you beat him, he turns into Geezernort. Right when he tries to split Sora's heart, Lea appears. So does Saix and a new Organisation XIII, hood down. Xehanort says, "Seven lights, and thirteen darknesses. You will face each other in that land." Then he disappears.

The last boss is armoured Ventus. Sora keept on sleeping, so Riku went to save him. You play a game where you have to put the pieces of Sora's heart back together, by hitting Sora's as they float gently down. Then you fight armoured Ventus there. Even if you win, Sora drops into the darkness. Then, Riku uses Sora's Keyblade. Then, Roxas (What are you afraid of?), Ven (What’s most important to you?) and Xion (What do you want outta life?) question you one after the other, giving you three options. After that, Ansem the Wise shows up. This is all in Sora's heart, bu the way, and he's there because of the research data that was put in there.

Ansem tells you that those three's questions are the key to waking up. Sora wakes up, and Riku is the only one acknowledged as a Keyblade Master. When Lea helped Sora, he wasn't able to produce a Keyblade, but right at the end he pops one out and everyone is surprised. Sora leaves alone on a journey and that is the end.

After the ending, you see Sora playing with a Dream Eater in Traverse Town. Right after, they show an image of Ven sleeping in Castle Oblivion.

The Organisation are Xehanort's tools. It seems that was their purpose from the start. It seems like the plan was to turn all of them into Xehanort. It looks like Lea is now 100% your ally, saying he's become a Keyblade Wielder and everything. At the end you see him off at Yen Sid's place, probably cause he still has training to do.