"Alone is what I have, alone protects me."Those were the last words he had uttered to John. They had been cruel words, but utterly necessary. He would not have left him otherwise but he needed John gone and he couldn't bring himself to be the one to walk away. He knew what was coming; Moriarty wanted him destroyed, wanted the heart burnt out of him, and John was the way to his heart.
He had to do this alone. He couldn't risk John falling into Moriarty's clutches again, not like last time. Sherlock had been scared then- beyond scared- he'd been terrified, he didn't want to lose John. John. His John. John who was so loyal, so quickly, so understanding and so kind. Who had never asked Sherlock to change, but had managed to make Sherlock a better person and a better man. He'd never cared what other people thought of him but he found himself caring about how his actions affected John, which was why he hated this so much. Hated what he had to do, hated Moriarty for making him do it but mostly hated himself for what it would do to John. But he had to, to protect him.
He knew Moriarty wanted him destroyed, but he'd never fathomed the true meaning of that destruction, and the rage driving the man behind it. From the very beginning he assumed Moriarty wanted him dead, but it was so much more than that. He wanted everything that Sherlock ever was torn down, his legacy and credibility obliterated. He wanted his one enemy destroyed so he could be king again. And that's exactly what he'd done.
The evidence against Sherlock had been piling up; everyone would soon turn against him. Everyone but John. Because John was loyal, because John knew him, for real. John stood by his side throughout everything and he never gave up. That's why it had hurt so much to drive him away, knowing he might not see him again for a long time.
John's parting remark "Friends protect people." reiterated in his mind throughout his encounter with Moriarty. It grounded him, reminded him of why he was doing this. He assumed John would be used as a weapon against him, it had worked last time after all, and he was glad to have deduced the outcome of Moriarty's plan soon enough to make preparations. He had finally worked out the final problem. But now, standing on the roof of St. Bart's looking down at John his heart clenched.
No matter how hard he tried, no matter what he said, John would not believe he was a fake. But it would be easier for John that way, to believe it had all been a trick, just a magic trick. He would be angry at Sherlock for lying, not heartbroken because he'd lost his best friend. But it hurt so much to lie to John, to listen to the pain and the disbelief in his voice, but he had to do this. He had to jump to save him. His blogger, his doctor, his friend.
"Goodbye, John."
Tears clouded his vision, and only one thought went through his mind, please God, let him live.