John's room was always messy, but Sherlock's was always clean. This was for three specific reasons.
1. John liked having his own space so he liked keeping it any way he pleased. He hadn't had his own space in years, from being in the service, and for those years everything had to be perfect. But now he didn't have to, so he kept it how he pleased.
2. Sherlock's room had hardly anything in it because he kept all of his crap everywhere throughout the apartment. Sherlock had a bed, a side table, a chair, and three shelves hanging on the wall next to the window. On the shelves were random keepsakes from the cases, including the pink phone, a can of the yellow spray paint, John's ear wire from when he was strapped to Moriarty's bomb, and also his skull, which John begged him to keep out of the living room.
3. Sherlock never took his belongings back to his own room after occupying John's room. He'd never take the dirty clothes that John stripped off him every night, he never took the papers he'd read after John's gone to sleep, John's lucky he even took his laptop back to the living room or his room. Half of the reason John's room was messy, it was because of Sherlock.
But John didn't particularly mind. He liked his room, his small area in the flat he occupied with the best man on the planet. Anything Sherlock brought home was left in the living room, unless he wanted to keep it close to him in his room. Often John slept in Sherlock's bed for this reason. Sherlock brought him home and kept him safe in his room just like his other prized possessions.
The last one bothered John more than he showed. More than half of the stuff in his room was Sherlock's. This would be annoying when Sherlock would hurry around the flat trying to find a certain thing but couldn't and it ended up being in John's room. This usually happened with clothes.
"John, where is my blue scarf?"
"Your blue scarf?"
"Yes, that's what I said."
"I have no idea."
"Can you find it?"
"Is there any reason you can't?"
"My neck is too cold."
Two hours later it was found on John's bedroom floor.
"This wouldn't happen if you took your stuff out of my room." John said.
"This wouldn't happen if you cleaned up your room." Sherlock said.
"This wouldn't happen if you didn't leave your stuff in my room." John said.
"This wouldn't happen if you just got me undressed in my own room." Sherlock said.
"Sorry, I like to sleep in my own bed after."
"So don't complain that my stuff is in your room. Why would I go to my own room and leave you alone?"
"All I ask is for you to take it out when you're done."
"Why don't you just stay in my room?"
"I like my bed."
"Why don't you…"
Silence.
"What, Sherlock?"
"…move your bed into my room." He looked at John with his big gray eyes that were sparkling with the pathetic, almost fearful, look in his eye. He bit his lip and tilted his eyebrows up, trying to look as pathetic as possible.
"Oh, don't give me that look. What, do you think I'll say no?"
"Well," Sherlock looked down.
"That's fine, Sherlock. I never got why we have separate rooms anyway." He tilted Sherlock's chin up towards his, "And this way, maybe we'll only have one messy room."
Wrong. The mess continued. Now their room was always messy.