A/N I know it took me a while but here are the promised alternate endings. –Lyn

He Picks Sherlock

John sat on the couch and thought about the situation he was in. Moriarty had kidnapped him, raped him, and tortured him. And John had thought that Moriarty cared for him…. God, how could he have been so blind? Stockholm Syndrome wasn't something he had expected to experience, that may be why it took him so long to see what it had done to him. But when he thought about how Moriarty was gone, and how even with all the crap that John had put him through Sherlock was there, ready to pick up the pieces all over again.

"So you've made your decision then?" Sherlock asked, well, said really as he already knew the answer. John nodded unnecessarily and he looked down at his shoes and clasped his hands together.

"If… uh… if you'd still let me stay." He said softly. He knew that he didn't deserve to stay but… a tiny, tiny part of him still hoped that he would get a second chance. Sherlock plucked a tune out on his violin and that was the only sound in the flat, silence stretching out all around them but the violin tearing down the silence between them in a not-so-unpleasant-way. "Alright… I get it. I'll leave." John said as he stood. He was sad, he had picked Sherlock… but had he picked wrong?

"What makes you think I want you to leave?" Sherlock asked in a mild tone. John looked at him curiously.

"Well you didn't say anything so I assumed that was my cue to leave."

"No, that was your cue to go and get more milk. I used the rest of it on my last experiment." John smiled and shook his head at his flatmate.

"Alright Sherlock, alright. I'll go and get more milk." John said, still smiling that ridiculous smile. He was just so happy that Sherlock had picked up the pieces again.

"John, I'll always pick up your pieces. Just like you picked up mine. That's what friends are for after all." Sherlock commented easily, still plucking at his violin.

"How did you-?"

"I deduced it. Obviously."

"Of course." He zipped up his jacket and opened the door.

"Oh, and John?"

"Yes?"

"Try not to get into any rows with the machines okay?" John threw him one last smile before nodding and heading out the door, closing it behind him and walking down the stairs to the street. He hit the sidewalk and merged into the rest of the foot traffic with that grin still on his face.

Everything was as it should be.