Author's note:

Whoa...this took way too long. So, in my headcanon, after Mary shot Sherlock and her secret was revealed to John, I think John probably moved back into 221B until he and her met again during the Christmas with the Holmes' family scene. You can see this as a continuation of "Back to Baker Street", the two kind of follow each other time line wise, but it doesn't have to be.

I guess this is kind of what the Johnlock fangirl in me desires had happened instead of John forgiving and going back to Mary.

I tried really, really, really hard not to make them too out of character (at least for chapters 1-3), but it ended up with John and Sherlock dancing around (took me 30 pages to get them to a confession T_T).

As for time line, I used John's official blog as a guide;
Wedding - August
Beginning of His Last Vow and Sherlock getting shot - September
Beginning of this story - November

Chapter 1 warnings:
Not-so-nice things about Mary, divorce, Johnlock, long-windedness, thickheaded characters, overuse of adjectives, long paragraphs crappy titles.

DECISIONS

The cool November air breezed through the room, fluttering some of the loose papers that laid about, but it barely seemed to faze the man who sat at the desk, staring blankly at the open laptop in front of him. He couldn't believe it, just over four months after his wedding he was sitting here looking into divorce proceedings.

It had about three months since that nightmarish night when he had found Sherlock lying in the office of Magnussen, hole in his chest and near death's door. Not even a week later his happy, if somewhat dull, home life had been mercilessly shattered. Mary's secret past life had been brought to light and she had given him that blasted USB, the USB that seemed to have the power to make or break his entire life. John had kept it with him wherever he went for weeks. He yearned to read what was on it, but at the same time he feared it. He didn't want to know. If he didn't read it, he could keep his illusions, keep imagining, keep believing that whatever Mary did hadn't been as bad as she had made it sound.

After Sherlock had been released from the hospital after his bullet wound finally healed enough for him to move around with relative ease, John had decided to move back to Baker Street with the detective. He needed to get out of his suburban house, away from Mary, away from all the memories of their happy times together. He needed to think clearly, keep rational and map out all his options. On top of that, he needed to be with Sherlock and make sure the man stayed on his meds and took care of his health. John never wanted to find the man back in a drug den, high under influence ever again.

Initially, Sherlock had kept mostly silent in regards to John's personal problems. He didn't attempt to pry and kept himself busy with his experiments since Lestrade was keeping him away from cases until he had fully recovered. Several times John had started to ask him for his opinion about what he should do. He knew Sherlock with his coldly calculating mind would be able to look through all of the emotional baggage that hindered something like this and find a rational, logical solution with ease, but each time he had snapped his mouth shut at the last minute, feeling guilty about burdening the man with more troubles relating to Mary. Sherlock had already put up with enough, this was John's problem now.

Once in awhile Sherlock would offhandedly allude to Mary, reminding him of some joke she had made, or some fun times they had shared together, and John knew it was Sherlock's attempt to encourage him to forgive her. But John couldn't shake the image of Sherlock on the floor that night, gasping for air, Sherlock in the ambulance, his heart giving out, Sherlock in the hospital, eerily still. He remembered all too well the fear that gripped his heart when the doctor had informed him that Sherlock had flat lined on the operation table, the grief that engulfed him when he thought he had lost his best friend again, and his anger at Mary, at the woman who had helped him through it all the last time but then so willingly put a bullet into the chest of his best friend. Sherlock may be convinced she didn't aim to kill, but John was having a hard time believing it given that Sherlock had, in fact, died. How she could still even look Sherlock in the eyes after what she had done John really didn't know, but for some reason it angered him and even seeing her in the same room with Sherlock had brought about a protectiveness in John towards Sherlock that even surprised himself.

He never considered Sherlock as someone who needed protection. The man was always so self-assured, he always had a plan, an ace up his sleeve, some trick to get out of even the most hopeless situations, but this time, this time John had realized just how human Sherlock really was. He was flesh and blood, he could bleed, he felt pain, his heart was not made of stone but of the same hot blood that ran through all humans. When he had pressed his hands over the bullet wound in an attempt to staunch the blood pouring out the warmth of the liquid seemed to almost burn him. This was the life of the man who meant the most in the world to him, spilling through his fingers, slipping away. He could still feel that warmth sometimes, in his nightmares he would sometimes look down and see the dark red staining his hands as anguish overcame him.

No. He needed to make a decision. He loved Mary. But not the real Mary it seems. Heck, he didn't even know her real name. He loved the illusion that was Mary. And while he's not willing to check through her records to see exactly what kind of person he had made a vow to love and protect until death does them apart, he was not willing to spend the rest of his life with an illusion. He didn't know if she was an assassin, some free lance killer, or some secret agent for a government somewhere, but she had been willing to put the life of the one man he cared about more than any others in danger, to protect herself, her secret. She can twist it all she wants as having done it for John, but John would never wish for harm to come to Sherlock. Never. That alone should be enough for John to make a decision. If she had loved John and trusted him as she claims, then she should have come clean. She should have told him everything before any of this happened. The only reason that Magnussen was even capable of blackmailing her was because she had secrets to be kept. Sherlock could have helped her, she knew he could, but instead, she had been afraid that Sherlock would reveal her secrets to John. Her distrust in John's ability to continue loving her because of her past dictated her actions of the present. Whatever she had been, it is clearly not simply part of her past. It is still very much a part of her present.

The short haired man clenched his jaws and refocused on the computer screen. He scrolled through the UK government's website, looking up the procedures he needed to go through to file for divorce. Apparently it seems, a divorce can only be applied for after a year of marriage. Blasted. An annulment can be applied for at any time, but John didn't have the necessary grounds for an annulment. His mouth twisted in a bitter smile. Who was he kidding. He had every grounds for an annulment. His wife had lied to him about everything, he didn't know who he was getting married to. But to apply for an annulment on those grounds would mean that Mary's past would be thoroughly investigated, and that wasn't something John wanted. No. He'll wait out the year then apply for a divorce. He doubt Mary will put up much of a fight against it. And the child...John paused. What about the child? Their child? Will they have shared custody? Or should he apply for full custody? Mary was the mother, but John grimaced thinking about HIS child being brought up by a killer. However, from what he's seen, he had no doubt Mary would love the child and care for it as any loving mother would. He had no reason to fear that the child will be in any danger under Mary's custody. He sighed. He'll deal with that when the time comes, right now he simply didn't have the energy to worry about so much. Besides, many children grow up with divorced parents and turn out fine, he can't force himself to sleep in the same bed as a killer in the hopes of maintaining an illusion of a happy family for his child.

John was so wrapped up in his thoughts that he didn't notice the soft footsteps that had snuck up behind him. Suddenly, he felt the presence of another person leaning over his shoulder and he gave a start, almost smashing his head against the other person in his haste to look over. Sherlock's pensive face was right over his shoulder, staring at his screen and glancing over the contents. The man was still in his dressing gown, barefoot and looking like he had just gotten out of bed. Quickly John minimized the window he had open although he knew Sherlock had seen everything. He forced himself to smile as he turned halfway in his chair to look up as the other man straightened up.

"Good morning. Did you eat? I left some toast for you."

Sherlock met his eyes but remained silent, his expression showing no hint of merriment.

"John, you shouldn't."

John decided to play dumb.

"Oh come on, if I didn't cook you know you'd starve in this place."

Sherlock didn't rise to his bait. Instead he pressed his mouth into a thin line, glancing between John and his laptop.

"You finally have a family, John. It's what you've always wanted. You shouldn't give that up for..."

Sherlock didn't finish the sentence, but John knew what the end was. 'You shouldn't give it up for ME' was what Sherlock wanted to say. The man seemed to believe wholeheartedly that any decision John made that separated him from Mary would be due to Sherlock. Truth be told, what happened to the detective did play a large role in John's decision, but it wasn't the only reason behind it.

"Sherlock, stop. This is my decision. I wanted a family, yes, but not this. Not. This. So stop guilting yourself that it's your fault."

Sherlock looked slightly offended at the accusation that he had been 'guilting' himself. With a sigh he backed away and plopped himself down in his chair, pulling his feet up to rest on the seat and wrapping his arms around his bent legs.

"Have you told her? Of your decision."

John kept his eyes on the man, he had seemed so much more subdued since the whole incident had happened. No longer did he flail about complaining about being bored, no longer did he go out to Barts to steal body parts for experiments, no longer did he play the violin, letting the melody meander through the small flat, no longer did he revel in showing off his observational skills and awing John with his brilliance. He'd sit in his chair for hours, simply staring into space, sometimes he seemed almost nervous to be in the same room as John, preferring to flee to his own bedroom and staying there until John forced him to come out for some food. When John would mention some new mystery stumping Scotland Yard in the news papers Sherlock would simply utter 'dull' or 'boring', sometimes throwing in an insult or two towards the intelligence of NSY. But John was pretty sure that when he was alone he would contact Lestrade about them, because several times he noticed that the cases in the papers that he had brought to Sherlock's attention one day would suddenly be solved a few days later, thanks to an 'anonymous tip'. John wondered when did Sherlock stop using him as a sounding board for his deductions. He missed those times when Sherlock would be at his finest, eyes gleaming like a predator on the scent of a prey, stalking, adrenaline pulsing through his veins, ready to pounce and attack. He wanted to ask the man exactly what had caused this change, but for some reason he wasn't sure how to start. What could he say? 'Why are you not the brilliant maniac anymore?', hardly a good conversation starter.

The older man shook his head and turned his eyes to study the fireplace.

"No. Haven't had a chance to yet. Will need to...set up a meeting sometime."

Set up a meeting, with his own wife. How lovely.

Sherlock gave him a once over, noting the defeated look on the shorter man's face. Clearly he hadn't been sleeping well, the dark circles under his eyes were a dead giveaway. He's lost weight too, Sherlock had no illusion that John only kept eating three meals a day because he needed to force Sherlock to do the same, and even then he would pick and prod at his food. Over the course of the past few months Sherlock has seen the man go from anger, confusion, grief and now it seems, finally, acceptance. Sorrow and acceptance. Sorrow at the decision he has to make. Acceptance that he has to make it.

Although they were both back in the same flat Sherlock wasn't sure exactly how to handle the situation anymore. He had never been good with human interactions, and the bizzareness of their situation made it all the more difficult to deal with. He wanted to support whatever decision John made, but at the same time, he didn't want to be the cause of the break up of John's marriage. John chose Mary, he loved her, even Sherlock could understand that. Whatever chemical reactions that constituted the feeling humans labeled as 'love', John felt that for Mary. He saw the way John looked at the woman, the joy she brought to him, and he had seen the same in Mary. Sherlock didn't quite understand the need for love, but clearly it played a significant role in the lives of most people, John included, and he was willing to accept that. Two people, in love, and with a child on the way to boot. The only wrench in their happy union had been him, he had to go storming into Magnussen's office, thinking himself a brilliant genius, only to find that his deduction had been wrong and the one who was threatening the man was not Mrs. Smallwood. He had been the one that blew Mary's cover, if he hadn't been so overly confident in himself, if he had just taken a second to think, then Mary could have kept her cover and none of this would be happening.

Of course after that he had to let John in on the secret. Clearly he had been shot in the chest, meaning he had seen his shooter, and he had no doubt John would demand for him to reveal his shooter. He might have even gone to Mycroft to aide in his search if Sherlock had kept silent, and Sherlock couldn't be sure that Mary was clever enough to escape Mycroft's prying eyes. On top of which, who knows what actions Mycroft might take if Mary's secrets were unveiled to him. No. Better John heard it from Mary herself than to find out from Mycroft. So he had set up the meeting in the alley, away from spying cameras, where only the three of the could hear the secrets of one Mary Morstan. No. Mary Watson. He knew it would be painful, he had been prepared for it, but even still, he couldn't help the wrench in his heart when he heard John's voice cracking demanding to know why his wife had turned out 'like that'.

/Because you chose her./

Sherlock's own voice echoed in his mind. His answer to John's heartbreaking question.

/...you chose her.../

Sherlock bit his lip to refrain from pointing out that at one point, John had chosen him too. On that first night together, instead of ignoring his text for him to come to Baker Street if convenient or even if inconvenient, John had chosen to come. He had chosen to. He had had no reason to. What person in their right mind would go running off to meet someone who they had only known for less than 24 hours knowing that it was dangerous? But John had. John had made that choice to. Just like he made his choice this time. Granted Mary hadn't sent him a text so blatantly stating that it could be dangerous, but John had been drawn to her unconsciously, drawn to the danger that swirled around her, like the danger that enveloped Sherlock wherever he went.

"You should think it over. It doesn't make sense to divorce her, she's no danger to you or your child. There's no logical reason for a divorce. You'll only make yourself and her miserable."

John furrowed his eyebrows, staring at Sherlock in disbelief.

"Doesn't make sense? Doesn't make sense? Sherlock, she SHOT you! She LIED to me! About EVERYthing! I can't think of anything else that makes MORE sense!"

Sherlock shrugged.

"But she's not danger to YOU, John. She would never hurt you. She did everything she did for YOU. That's how she shows her love for you, that's how she protects you, because she knew if you found out about her past, this...grief would be what you would feel. This is exactly what she didn't want you to feel."

John shook his head.

"That's just...twisted. She could have told me before, she could have let me make the choice, but she chose to lie instead."

"Oh please, John. This isn't exactly the kind of conversation someone just slips in. When was she suppose to tell you? When was she suppose to pull you aside and tell you that 'Oh, by the way, I was an ex-secret service agent in the past and my name's not really Mary, but I can't tell you my real name because you'll hate me'? Do think about it John, what you're saying is the romantic side of you talking, but it's simply not realistic."

John growled in frustration.

"Well that doesn't make what she did OK. None of those are good enough reasons for lying about something so profound, and then almost killing you on top of that."

Sherlock stayed quiet this time. He unconsciously rubbed at where his bullet wound was. It still irritated him sometimes, and if he stretched the wrong way it still hurt, but it generally didn't disrupt his daily activities anymore. That had been his first time getting shot at such close range, and it really had hurt a lot more than he had expected. Even the beatings he got in Serbia seemed mild in comparison. This pain was so much more intense, and the searing heat as the bullet entered, it had felt like it was burning him from the inside.

"Stop that. You'll only irritate it more."

John scolded gently. He knew all too well what bullet wounds felt like.

Sherlock couldn't help but pout slightly. It was itchy and he wanted to scratch.

"Sherlock, stop that right now. You know you can't scratch it. If it's too itchy then go put some of that ointment on it."

The detective rolled his eyes.

"That stuff gets all over my shirts. I've already ruined several thanks to it."

John raised an eyebrow.

"Well...just wrap some gauze over it then."

Sherlock let out a long suffering sigh as if John had asked him to do something absolutely horrid.

"That impairs my movements. It's gets in the way. Plus it's uncomfortable."

John sighed, sometimes taking care of Sherlock was like taking care of a child. He threw tantrums at the littlest things, and usually without warning.

"Well, either way, stop scratching. It's just healing up, so let your body do its job. The itchiness will go away in a few more weeks."

Sherlock looked at him in horror.

"A few more weeks?! You're not serious!"

John's mouth tilted up in a sympathetic grin.

"Dead serious. Sorry."

Sherlock leaped out of his chair with an exasperated gesture of his hand, running the other one throw his wild curls.

"ARGH!"

John couldn't help the amused little chuckle that escaped his throat as he watched Sherlock storm into the kitchen, snatching a piece of toast and jamming it in his mouth, chewing as if the toast had offended him somehow.

"Keep scratching and it'll be even longer."

John informed him helpfully, only to be answered by one of the kitchen gloves being thrown at him. It smacked him on the head then flopped harmlessly to the floor. That caused John to laugh even more, the sound seeming strange since he hadn't laughed for a long time. Sherlock paused as he saw John laughing, a small grin spreading over his own face even though he tried to hide it behind his toast.

Well, maybe things will work out.

Found the information about divorce and annulment on the government of the UK's website (it seems I can't post URL here, but if you really want to know the details just do a Google search for UK divorce and annulment and you'll find it.)

Thanks for reading! Comments and reviews appreciated as always!