Summary:

SPOILERS FOR SEASON 3.
Alternate ending for the scene in the train carriage full of bombs.

Time had stopped. Everything was silent, except for the thumping of Sherlock's own heart in his chest.
He was in abandoned train carriage which had been turned into a huge bomb and it would be blown up less than two minutes. He was there with John, one of the few persons in the world he cared for a lot and he felt such pain and guilt doing this to him, but he had no other choice. Because of course the bomb wasn't going to explode and they weren't really in life threatening situation, although John still believed that. Sherlock had found the off switch from the bomb in about 4 seconds, but he had to do this. He needed to hear John's forgiveness out loud and what would be better way to make him say it than put them in life danger? Sherlock couldn't think of anything better and therefore he let John still think they would be both dead in matter of seconds so he would hear the words he needed to hear the most. Sherlock's heart was thumping even louder in his chest.

"You were the best and wisest man that I've ever known... Yes, of course I forgive you."
John had turned his head away like he was ashamed of what he just blurted out, but Sherlock was now watching him with an awed expression on his face. Those words had hit him hard, he had needed them even more than what he thought. Sherlock stood up slowly, realizing right then how John was preparing for the explosion which would never come. He had took a hold of one of the poles and had closed his eyes, looking sad but quite calm considering the situation.
Sherlock wasn't even sure what he was doing, but he wanted to comfort John and also thank him for what he had just done to him, but of course he wouldn't actually say it, that wasn't his style. Instead he took John's hand in his own and squeezed it gently, and when John opened his eyes in surprise, he also flashed a faint smile to him. What happened next took Sherlock by surprise, but he didn't resist at all when John's lips were suddenly against his own and he could also feel a hand behind the back of his head, caressing his hair softly. Sherlock kissed back, until John pulled back after a while.

"Sherlock."
"Mmh?"
"Why haven't we exploded yet?"
"Oh, right. Sorry about that. I found an off switch the moment I checked the bomb, it's not going to go off. Oh and also the cops are on their way so we can go now." Sherlock answered while already putting gloves on his hands and making his way out of the train carriage.
John was too dumbfounded to say anything and Sherlock couldn't help the grin that was spreading on his face because he knew exactly how John would look right at this moment, even though he didn't even see him. He didn't need to, he knew his John too well.
His John. He liked the idea.

After 20 minutes of listening complaints, accusations and scolding from John while they were walking out of the train tunnels, Sherlock finally spoke again.

"...you have any idea how scared I was? That was so unfair, I'm so going to-"

"Are you hungry?"
"I- what? Have you been listening to me at all? Seriously, Sherlock I...! Yes, I'm starving actually."
"Good. There's a really nice restaurant just around the next corner, we should go eat something. And maybe some wine to you, that babbling is really getting on my nerves."
"Babbling?! To YOUR nerves!? Excuse me, Sherlock, if I'm a bit shaken after what you just put me through! I swear to god, if-"
"Yes, yes. So here it is, get inside please." Sherlock opened the door for John politely and flashed one of his trademark smiles to him, getting only a frustrated huff from John back. Sherlock knew he wouldn't need to beg for forgiveness for this one, John had been just as relieved to get those words out too.

They had been eating their dinner mostly in silence and John seemed much more relaxed after few glasses of wine and a good meal. Sherlock stole a glance every now and then, just to make sure his John was alright. He wasn't really hungry himself, but knew John too well and buying a dinner for him would get Sherlock's position as the best friend back for sure.
John was finishing with his food and was wiping his lips with a napkin and Sherlock was fighting an urge to lean in to kiss those pouty lips again.
John seemed to be thinking about kissing too as Sherlock learned when John spoke again.

"So, about the kiss earlier..."
"Yes?" Sherlock put his hands together waiting for John to continue, like he was listening one of his clients about a new case.
"Can you not?" John rolled his eyes.
"What?" Sherlock tried to look innocent, but changed his bodylanguage to make sure for John that he was actually listening and interested on what
John had to say. He crossed his legs and crossed his fingers over his knee.
"So, I just wanted to say..." John cleared his throat and was fidgeting with the napkin.
"I just wanted to say that I wasn't really thinking straight at the moment and -"
"Nope, not straight at all I agree. I think it was quite gay thinking."
"Shut up, Sherlock. I'm not gay!"
"Me neither."
"Yes, well anyway. I just thought we should talk about it, because -"

Sherlock was trying to hold a burst of laughter and John was getting more red with every passing second.
"Are you enjoying this? Is this funny to you? I'm trying to-"
And then Sherlock lost it and was giggling like a little school boy in a situation where you are not supposed to laugh. John was opening and closing his mouth like a fish out of the water. He tried to say something, but the words wouldn't come out. Sherlock was trying to calm down and John used the distraction on his advantage and ordered some more wine from the waiter.

"Sorry, sorry. Continue please." Sherlock managed to say while still wiping his eyes with a napkin and trying to get himself under control again.
"What was so funny?"
Sherlock turned to face him straight in the eye and he wasn't laughing at all anymore.
"Nothing what you said. Only how difficult talking seems to be to you sometimes. It was just a kiss." And Sherlock leaned back again, leaving John speechless for a minute. The waiter came with a full glass of wine and John thanked him, gulping down almost the whole glass with only one sip.
"Just a kiss. Right. So it didn't mean anything to you?" John asked, trying to sound casual, but couldn't face Sherlock, watching the glass of wine instead.
"It did." The answer was so simple, but meant so much. John turned his head slowly, until their eyes met.
"So are we done? I'd gladly get home already, been a long day." Sherlock said and he didn't need to act casual. Everything was always casual to him. Maybe that was why everybody fell in love with him, all that confidence and charm in one package would make anyone's knees jello.

They stood up and went out. It seemed John didn't have anything more to say to the previous matter, or to anything else either so they walked silently towards 221B Baker Street.
"You want to come over for the night?" Sherlock asked when they had been walking good five minutes or something and neither one of them had yet said anything.
"Well, I could.. I mean, if you don't mind. Mary isn't home tonight anyway and.. So if it's not too much trouble."
"You can come, there's plenty of room and Mrs. Hudson would love to have you back." Sherlock glanced at John and smiled gently to him. Like he didn't ask this because of himself, but for Mrs. Hudson, yeah right. He wanted to have his John near him again, where he could see him, touch him and protect him. They continued their walk for another 15 minutes in almost complete silence, just John babbling something random every now and then which only got "mmh" or "right" back from Sherlock. Until John asked something that woken up some butterflies in Sherlock's stomach, a feeling that he hadn't felt maybe ever before.
"So would you like to.. you know, maybe.. kiss me again? Sometime..?"
Sherlock stopped and so did John.

"Would you want me to?"
John maybe tried to outsmart Sherlock and quickly bounced the question back at him.
"Would you?"

There was no other sound but the heavy breathing of the two men facing each other in an dark alleyway. Sherlock's intelligent brains were working full speed and in 5 seconds he had already thought all the possibilities and options he had and he knew exactly what to do. He didn't need to say anything, he didn't need to ask anything more, he knew exactly what he wanted, but he also knew exactly what John wanted. So no further questions or talking wasn't needed, just actions, emotions, feelings, and at that moment Sherlock was vulnerable for the first time in his life. He let his walls down and his eyes were so soft, full of love, caring and other mixed emotions.
At that moment his light blue eyes were shining so brightly and they were as deep as the ocean and John's jaw dropped a little in awe.
Sherlock's face came closer and closer, but John didn't back away even an inch, but waited patiently. Waited for the moment when their lips would collide and he could taste the man he loved so much. And then it happened, their lips sealed together and they kissed each others like the world was about to end. Sherlock grabbed John by his jacket, gently but firmly and John loved the feeling being submitting to the taller and more intelligent man, but he also loved how gently Sherlock was kissing him. With so much love and passion it made John's head a bit dizzy.
Time passed by, but they didn't even recognize it, neither one wanted to end the kiss so they just let their tongues linger in each other's mouths, exploring and caressing.
They pulled back for brief moments only to get back at what they were doing second ago, and Sherlock felt like he could go on forever. He wouldn't care if the world ended right now, because he would die happy, in the arms of the man he loved the most.
Who knows how long the kiss would've go on if they wouldn't be interrupted by a flashing light. And then another. And another. And they had to cover their eyes so they could better see what was causing the flashing lights around them. Paparazzis.
"Oh no, oh my God no no no, GO AWAY YOU FUCKERS!" John exploded horrified.
"Come." Sherlock's firm voice was reassuring near his ear and he let him walk him away from the situation, hand in hand. The paparazzis were buzzing with excitement behind them, but luckily they didn't follow them. Maybe they already got what they wanted.
"Oh God, Sherlock, what do we do now? This will be on tomorrow's papers and people will think... people will think I'm gay!"
"If you haven't noticed, I'm actually a man. And as far as I know so are you, so I'm sorry John, but with my logic you are gay."
"No I'm not! It's just... You're different!" John huffed waving his hands frantically making him almost seem like a maniac. But soon his hands dropped and he freezed totally.
"Oh my God... OH MY GOD, Mary will see this! I've been cheating Mary and she will read about it from the newspapers! Oh my God, Oh my God..." John was in the verge of hysteric, but for once Sherlock didn't know what to say. He didn't care what the papers were writing about himself, but he didn't want John to be put in a bad light. And the papers would absolutely LOVE the lovetriangle between the world's best detective, his male companion and companion's soon-to-be wife. Sherlock felt awful for his John.
"What am I going to do Sherlock?" John sounded desperate and sad, and Sherlock's mood dropped one more level.
"You are going to tell the truth to Mary, tonight. She's a clever and compassionate woman, she will forgive you, she will understand. You'll marry her and make babies and live happily ever after." Sherlock's heart ached more with every word he let out of his mouth, but all he wanted was John to be happy. He only wanted what would be the best for his John, and he really seemed to love and care about this woman. And to be honest, Sherlock liked her too.

"But... but what about you? What about you... and me?"

"We can stay friends, just like before." Another piece of Sherlock's heart fell off and broke on the cold ground.

"But... but I..."

"But you what, John?"

"I... I love you."

A moment of silence. Sherlock turned around to face John.
"I love you too, John."