Sherlock was obsessed with John's body.
He pulled up pictures of them taken by the press, marveling at John's squatness in comparison to his length; the paradox that they could each simultaneously command the image.
He stole bits to save: hair from pillows and nail clippings from the bin. Once, gloriously, a tooth, dislodged in a fight. Sherlock took a kick to the back in order to retrieve it.
After this the thought of losing John's body in any portion became abhorrent. It could change, it should change—representing new, stronger versions of John—but Sherlock couldn't bear for those past versions to be forgotten. He saved the jeans John discarded and kept a detailed journal of all his scents. Sherlock glared at John's scar because there were no pre-war pictures of him without a shirt and Sherlock would never know what his shoulder looked like without it.
John noticed, and sometimes he even accommodated the obsession, more so after The Return. He learned that after cases gone wrong Sherlock's desire to remember his battered body was not the same thing as wanting to see him hurt. People always said they wanted all of you, but only Sherlock meant it.
So John lay still. He allowed Sherlock to take a permanent marker to his side, tracing the outlines of fading bruises.