John was a trained killer thanks to the army. He had never actually killed anyone while he was out in the field but he knew how to if he needed to. The killing didn't start until he was back home in London after he was honorably discharged for being shot. The first time it happened John was in the middle of a flash back, he thought that he was back in Afghanistan being shot at. He had instinctively reached for his gun, (the gun he always carried with him) to shoot back at the enemy. The poor girl didn't even see it coming. She was walking in front of John, minding her own business. She was heading to work; she was already late as it was. John had shot her almost point blank in the back of the head.
The sound of actual gunfire brought John back to reality. It was then that he realized what had happened, what he had done. He couldn't believe it. Had he really just killed someone? His gun still raised in his hands, he began shaking. He wasn't quite sure what to do exactly; he most certainly did not want to go to prison right after got back from the war. He had finally found a flat mate, even if he was bit eccentric for John's liking. Nonetheless he liked his new flat mate because he was smart. Smart enough to take one look at someone and know everything about them. He also wasn't afraid to tell you either. John had thought that that was really cool.
John stood over the body of the dead girl thinking about what to do. He decided that as bad as it was he was going to leave the body. He made sure that he didn't leave any trace evidence that would link him to this girl. After that he phoned DI Lastrade telling him that he had just found a dead body near his flat. John had decided that his story would be that he had been walking to the store to get some groceries (the flat was somehow always empty) when he had found the girl's body. He knew that this would be a plausible enough lie, one that he knew Sherlock would even believe because John really was headed to the store. Lastrade even believed him, because as far as he knew, John was a good guy.
Lastrade had phoned Sherlock to come look at the crime scene, but it just made Sherlock mad because there was not enough evidence. Nothing to incriminate anyone, it looked as if the girl was followed; shot and the killer immediately ran away. But there were no foot prints, no fingerprints, no nothing. This made Sherlock livid. He hated crime scenes like this. So needless to say the crime went to cold cases. Sherlock hated cold cases; he hated leaving a crime unsolved. He also hated not having answers. John on the other hand felt a whole hell of a lot better knowing that the case went cold. John wasn't even a suspect.
As much as John felt guilty he refused to admit to murder.