EDIT: I have altered this story slightly to make it fall in line with the "Secret" Ending of Birth by Sleep since this is a canon story
Excerpt from Kingdom Hearts II:
The Death of Ansem the Wise
The Data Encoder beam started to flicker. "Ansem?" asked King Mickey.
Ansem the Wise laughed, "I'm a fool," he said, "I spent years studying the workings of the heart. Yet it seems I still haven't learned a thing!"
"What dya' mean?" asked Mickey.
"The process of encoding hearts is incalculable," said the old man, "The inhabitants of my Twilight Town were data created from real hearts. I was convinced that they would think and behave the way I had envisioned—but I couldn't have been more wrong." He hung his head in shame. "A heart is so much more than any system," he continued, a sense of wonder in his voice, "I saw it when Roxas and Kairi crossed paths. I knew, but I was too stubborn to accept it." He gritted his teeth. "It's always the same," he lamented, "I try to wrap my mind around things my heart already knows, only to fail." He looked up at the Kingdom Hearts high above. "While I was trying to bring Sora back, I had so many plans in store," said Ansem grimly, "But once Sora was an acting force they fell apart." The old king looked down in shame. "All my research amounted to nothing, compared with that one boy's heart."
The Encoder began to shudder and spark,
"Ansem," cried Mickey, "The machine!"
"All the more proof that hearts cannot be contained by data" said Ansem sadly, "Run my friend!" he shouted, "It's going to self-destruct, and anything could happen!"
"Your Majesty!" shouted Sora as he came running up to the monarchs. Riku, Kairi, Donald and Goofy following close behind.
Ansem turned to the Keybearer "Sora," he said, "the rest is up to you… And Roxas—I doubt you can here me—but… I am sorry."
"Ansem!" cried the mouse king.
Ansem looked at him with an expression of ultimate regret. "My heart is telling me what I must do. Please allow me to do what it says!"
"No!" cried Mickey.
Riku bent down to pull his old companion to safety. "Riku!" pleaded the mouse.
"His heart's decided," said Riku, "we can't change that."
A column of darkness arose behind the old sage, "I was wondering who would dare interfere with my Kingdom Hearts" said Xemnas, he looked at the assembled group. "And look--here you all are. How convenient for me." The Nobody's eyes fell on his former teacher, "Ansem the Wise…" he said mockingly, "You look pathetic."
"Have your laugh," replied Ansem, "I deserve as much for failing to see you for the fool you are."
"Students do take after their teachers," replied Xemnas, "Only a fool would be your apprentice. After all, none of this would have happened without you," continued the Nobody, "YOU are the source of all Heartless. It was your research that inspired me to go further than you ever dared."
"I admit," said Ansem, "my disregard brought chaos to more worlds than one." "But what were you seeking? You erased me from the world, only to take my name and continue research better left forgotten…. Is this the answer you were looking for?"
"All that and more," replied Xemnas, "I'm carrying on what you yourself began, and I'm creating a brand new world, one heart at a time." "I understand though" continued the Nobody, "unlike me, you have a heart. And you're powerless to control it. Consumed by the jealousy you feel for the student who surpassed you."
Ansem closed his eyes. "Xehanort," he said sadly, "Foolish apprentice of a foolish man. You have surpassed nothing—only proven how little we both know." The old king looked out into the darkness. "We may profess to know the heart," he admonished his former apprentice, "but its essence is beyond our reach. We're both ignorant—as oblivious as when we began. I'm afraid that any world you try to create…" he turned to the Nobody of the man he once knew as a friend. "Any world of yours… would be an empire of ignorance. That is why you and your creation are destined to fall!"
He turned back to the Encoder, "We've said enough!" he shouted. He looked to his young assistant, "Riku, you know what to do!" The sage turned to his friend, "King Mickey, my friend, forgive me." His eyes fell upon Kairi, the Princess of Heart for Radiant Garden, his little girl, now a strong young woman. What could he say to her, would she even know who he was beyond a pathetic old man in the last moments of his life. No, he decided, there was nothing he could say to her to make things different so at last he turned his eyes to the inevitable, "Farewell!" he shouted.
In that final, fatal instant, time seemed to slow to a crawl for Ansem the Wise. Scenes from his life flashed before his eyes… the day Xehanort came to his world… the experiments that brought ruin to so many innocent lives…the long war that turned the paradise of Radiant Garden into the blasted wasteland of Hollow Bastion… the plot against him by his own students, the murder of his wife and the exile of his daughter, while he was cast into nothingness….
All these memories and more he saw, and finally a light shone on Ansem, the pure, incorruptible light of Kingdom Hearts, and he sensed the hearts of all those he had loved, all those he had lost. "Kairi," he said softly, "Forgive me." And in that single instant, Ansem the Wise, the greatest king the world of Radiant Garden had ever known, a brilliant scientist who spent his life trying to quell the darkness of the heart, a poor old man whose lust for revenge had brought him nothing but misery and despair, vanished in a flash of light that illuminated all the worlds with its brightness.