An alternative way of how Sherlock and John reunite after Sherlock returns . John confronts Sherlock immediately with his question "Why?"
A short story how the conservation might have looked like.
(Please excuse my bad english - I'm not a native speaker)

Disclaimer: I own nothing.

„Sherlock … why? And don't you dare to make excuses. I just wanna know … why?" he tried hard to stop his voice from quavering and choking. But though his voice was one thing his body language was quite another. John was aware of his trembling hands, his clenched fingers, struggling for control, his sloping shoulders as if the burden he was carrying too much to bear. But most of all it was his eyes that mirrored the hurt and betrayal when he looked up at that one man standing in front of him. And he knew it, for God's sake; he knew that none of that failed to be observed by Sherlock. Though his friend (he flinched from the word) might not have a great understanding of the science of human nature he nevertheless knew how to deduce and interpret the signs of body language. And he bloody well knew that with every second passing by Sherlock kept reading him like an open book.
His crystal blue-green eyes rested calmly on him, impenetrably, waiting for John to regain his self-control.

When John seemed to have recovered a bit the detective opened his mouth for the first time, since they have entered the familiar apartment, they once used to share.

"Why don't you have a seat first?" with a straight face he pointed at some old moving cartons, covered in dust, which have never been taken away, though the apartment was left empty and vacant for so long now. John did as he was told. Not once averting his eyes from Sherlock's. Sherlock, however, remained motionless in the middle of the dark apartment, wavering what to say. He has always been a man of few words.

"Why did Molly know?" John asked finally when his friend made no attempt to start the conservation. "Why did she know?" And I didn't? Echoed his own voice in his mind but he didn't say it out loud. It did not have to be said. Sherlock knew anyway. The unspoken words hung in the thick air and both men felt its weight on their shoulders.

"She helped me fake my suicide."
John took in a deep breath. "That's not what I was talking about."
"Of course."
More tensed seconds passed until Sherlock finally broke the silence. "She was not in danger."
John furrowed his brow.
"John, you need to know that the day I chose to jump from the rooftop was not because of the lies and rumors that were spread about me nor because I had lost the game."
Now John was even more confused. His eyes were only small slits now. "Then why did you jump?"

"Before anyone of us had even arrived at the St. Barth Hospital I already assumed what Moriarty was up to that day. That's why I sent you away with the simple lie Mrs. Hudson is dying.
But I was still certain that I was going to be the winner in the end. I thought I'd beat him. I miscalculated as it turned out to be. I never considered Moriarty may choose this way to get me …"

"Which way?" John asked his voice barely audible.

" … The way through my friends." Sherlock threw a brief glance at John and then kept staring out of the window as he spoke.
"You were the whole time at gunpoint while I was standing on the rooftop. Lestrade, Mrs. Hudson and you. 'Three gunmen, three bullets, three victims' as Moriarty put it. They would have shot if I didn't jump." Sherlock forced a smile to conceal his discomfort.

But John didn't smile. Something had changed but Sherlock couldn't really figure out what it was. The anger and confusion in John's face slowly vanished and turned into an unreadable mask.
Sherlock eyed his friend closely but confused. He had expected a different reaction from him. Surprise, delight, gladness? Yes! But what did the long-reigning silence mean?
" … John?"
"No no no, Sherlock. No." John shook his head restrained. "Don't interrupt me."
"You weren't talking."
"I was thinking." John imitated his voice.
Sherlock stifled a smile.
After an even longer time John swallowed hard and eventually uttered: "You died … for me?"
"I'm quite sure I'm not dead. I've checked."
John snorted. "You idiot!" It sounded more like a compliment than an insult.
An immense feeling of relieve overcame Sherlock.
Once again they found themselves standing in the deafening silence. Only this time it felt a bit more pleasant. Both of them were engrossed in their own thoughts.

Indeed. John was standing there, in front of the man; he had mourned so long, and still couldn't believe that it was true. It all must be an awful dream.

"It's not a dream, John." Sherlock said with a crooked smile. John squinted and let out a snort. He wasn't used to that "mind-reading machine" anymore. But he had to admit he had missed it. For too long.