The words rang in her ears like bells, striking with every beat of her heart, every breath that she takes. "Did you miss me? Did you miss me? Did you miss me?" words that she had hoped would stay away for the rest of her life.
When Mary had met John she knew everything there was to know about him and Sherlock. She had known that he was grieving and soon she found herself loving him. That hadn't been part of the plan.
The plan had been to intercept, discover if Sherlock really was dead and kill if it came to it. But that hadn't been possible, Mary had followed John and discovered his daily routine and then, to get a larger insight, she booked an appointment with him in the surgery and there was a spark between them. She couldn't ignore it and John felt human again for the first time since Sherlock's death. Mary then found herself wanting to speak to him, comfort him even. Mary knew that Moriarty would have her head if he found out but she was falling for John and she had to try and abandon the original plan. She tried to reason with her boss but when it was clear that there was no feasible way out, she faked her death. Moriarty thought she was dead so sent some one else out to scout for information on Sherlock. Sherlock had thought he had cut off Moriarty's network off at the source but Sherlock had been right in the fact that Moriarty's network was a spider web with Moriarty in the center. When the web was brushed away, there were singular threads left with loyal people still attached.
The falling in love and marrying of John Watson had not been planned and was therefore punishable by their deaths for Moriarty. But none the less it had happened and now those words were reverberating in Mary's head. She had known he was alive but now it was clearly a matter between life and death. She couldn't tell John because he was still having trouble forgiving her for the secrets she had kept from before. Telling Sherlock would be a possibility and she knew that Sherlock wouldn't say anything to john as he cares for him just as much if not more than Mary did but that wasn't the problem. The problem was how to keep safe and that wasn't going to be easy.
"But, he shot him self in the head didn't he? He's dead!" she said in disbelief
"Well if he is, he better wrap up warm. Cause there's an east wind coming." John said this like it was fact. But Mary knew otherwise. If Moriarty was back and he knew that Mary was with John and Sherlock, he was after them and there was no way out.