When Sherlock 'died', John didn't leave 221B for a year, Lestrade came around lots to make sure he had everything he needed after he realized this. After a year, Lestrade managed to get John to come outside. He told Mycroft the news, they had started dating after Sherlock jumped, realizing they needed someone to fill the hole Sherlock left. Then Mycroft found out Sherlock was alive after 'accidentally' spotting him on a security camera. He never told anyone but managed to contact Sherlock, although he only text back twice, one asking him to keep updating him on how John was and the second a smiley face when Mycroft told him he left the house.
After John came outside, Mycroft told him he needed to sort his life out. John shrugged, not caring anymore. Mycroft said he would get him the surgery for his shoulder and he could go back to war, again, John shrugged. He gave John the surgery and afterwards, John seemed to realize he could join the army again. John had hope in his eyes when he asked Mycroft to let him back out in the field. At first, Mycroft was hesitant but in the end, he let him.
John was deported to Afghanistan the next day.
Mycroft told Sherlock. Sherlock almost came back to drag John from the war but Mycroft stopped him. Sherlock finished Moriarty's web two years later. He came back and sat at 221B until John returned.
Sherlock Holmes wasn't known to be an emotional person but when John returned, he couldn't help but shed a few tears.
John returned 3 months after Sherlock's return. He didn't go to 221B for another week because he was sorting out his life but when he did. He got the shock because no one had told him Sherlock was back. Or even alive. So he didn't expect to be attacked by a hug as soon as he passed through the door with a shout of 'John!'. Sherlock didn't expect to be punched.
"Three years, Sherlock. Three years." John said after the debacle in the hallway. Sherlock had the decency to look slightly ashamed, "It was necessary." John huffed, "Don't give me that bullshit, Sherlock. Why?"
"Moriarty was going to kill you."
"How?"
"That day on the rooftop, he had three snipers trained of you, Lestrade and Mrs. Hudson. I couldn't let you or them die because of me."
"Afterwards, Moriarty was proclaimed dead. Why didn't you come back?"
"Moriarty's web."
"Elaborate."
"Moriarty, he was the 'go to' person for all criminals. Like I'm the 'go to' person for the police. He was in on every scheme all around the world. He was the consulting criminal. The opposite of me so of course he had connections. His right hand man, Sebastian Moran."
John cut him off, "Sebastian Moran was from the army, excellent marksman. He got discharged when he got himself into a 'bad crowd' a few years ago." Sherlock nodded, "That's him. He ran all of Moriarty's connections until Moriarty came back, which wasn't long. But, by this time, I had took out a quarter of the web and Moriarty noticed immediately and ordered a rather large sum of money on my head for anyone who brought me to him. Alive. This got me into a few sticky situations but I managed to get out of most of them."
"Most of them?"
"A few of them kept me longer than I would have liked, one of them actually took me to Moriarty. Unfortunately, the main fault in any villain is that they talk to much and make to many threats. I got away eventually."
"Keep explaining."
"Anyway, Sebastian Moran passed messages from the healing Moriarty to his... Customers. By the end of two years, I had taken out or bribed most of his web. The only ones left were disposed of by Moriarty himself, they either got too close or they tried to kill him. Moran always took care of them. Then, there was only two left, Moran and Moriarty."
"How do you know they were the only ones left, or if they are dead?"
"Oh no, they aren't dead. Yet. I left them in very capable hands though." John shuddered, "Remind me to never get on your bad side."
"I doubt you could do that, John. You're my friend." Sherlock stated, "Moran and Moriarty were good at hiding. It took me another year to find them. They were hiding out in Australia, deep inside the bush. They had there own safe house there. After many days of traipsing through the bush, I finally found it. It took another few days to get inside, then I found them. I knocked them unconscious with a sleeping powder an accomplice gave me, very good stuff."
"Do I want to know who?" John sighed.
"Probably not."
"I won't ask then."
"Good plan. I handed Moriarty and Moran over to my specialist and they probably wont be seeing daylight for the next few years. Or the rest of their lives hopefully."
John sighed, again, still digesting all the information he was given, "You know they will probably escape, right?" Sherlock nodded, "It's a possibility but not as much as your thinking. Their earliest escape would be a few years at least. It took me a few years to get out. But he was testing me so he gave me food. They probably wont be getting much so it would take them longer."
John nodded, "I suppose. I have one more question, how did you survive?"
Sherlock shook his head, "I don't know myself."
A/N: SORRY FOR LEAVING IT AT SUCH A... A... ABRUPT ENDING. I couldn't end it so, yeah. I'll leave it to your imaginations ;)