I was just testing this out, I haven't written a nightmare story for Sherlock before so I thought I'd give it a go.
Sorry for any mistakes.
I'm also sorry if Sherlock seems a little out of character.

Nightmares certainly weren't a mystery to John. The ex-army medic suffered from them a lot and was used to starting into consciousness with the scent of blood mixed with sand still wafting around him from his subconscious. So when he awoke in the early hours of the morning to an obviously distressed scream he wasn't entirely worried, just a little tired of the monotony of waking in the middle of the night. That was, until he realised with a frown that he was suffering none of his usual post-nightmare symptoms. There was no sweating, no trembling and no feeling tearful. His warzone hallucinations weren't making an appearance. It was then that he connected the dots. He wasn't suffering from his post-nightmare symptoms because it hadn't been him that had been in the midst of a nightmare. The scream had emitted from downstairs. From Sherlock's bedroom.

John removed his covers as he heard a whimper rise up through the floorboards. He slid his feet into his slippers and made his way to the doorway of his bedroom running a hand over his face as he set about making his way to Sherlock's bedroom. Admittedly, John was a little apprehensive. Sherlock was a very private person who didn't take too well to be seen in a moment of weakness. John didn't think he'd accept being coddled too kindly. But his thoughts were lost as another frightened scream echoed around here otherwise quiet apartment and John all but ran down the stairs, pushing open the door to Sherlock's bedroom and flicking on the big light.

The emergence of light did nothing to rouse his flatmate. He winced a little as John entered the room, grimacing as he remained caught in the throws of the nightmare. He was tangled in his bed sheets, his top sheet had wrapped itself around his legs, the appendages trapped in the material. His bottom sheet had slipped away from his mattress, a sign of how much the man had been tossing and turning. His pillows were spread across the floor, one at the foot of the bed, one near his drawers and his head was flat against the mattress, his arms raised above his head, resting against his headboard. His duvet was half-on half-off the bed and from what John could see of the waistband on his pyjamas, his bottoms were at an odd angle and his pyjama top was twisted and raised above his belly button. The man was shaking, his body trembling and jerking as though he was trying to avoid something.

John was having an internal debate on whether or not he should wake his friend when the man turned again, his mouth opening slightly as he mumbled, his words only just discernable.

"J'hn." Sherlock spoke again and the doctor in question frowned slightly. Sherlock sounded hurt. "J'hn. Please. Stop." Sherlock hiccoughed a little as his breath caught in his chest and John felt a lump grow in his throat in realisation. His best friend was in the middle of a nightmare. And it was about him. "Please." Sherlock begged again, his voice weak.

John made up his mind. He couldn't stand to watch his friend suffering like this and knowing that he was the cause of it, no matter that it wasn't real, hurt him. He stepped forwards, gently speaking Sherlock's name and laying his hand on his friend's shoulder. When the man failed to be roused by the contact he shook him gently, squeezing his thin arm as he did so. John almost jumped when Sherlock awoke with a start, a gasp filling the room as his hazy eyes met John's concerned ones. Sherlock was tense but slowly, as he came to his senses, his eyes flickered closed and he began to relax.

"I woke you." Sherlock noted as he reopened his eyes, his voice hoarse. He lowered his hand and ran it over his face before tugging his pyjama top down. John couldn't help but notice how Sherlock's right hand was trembling slightly.

"Y-you were screaming, Sherlock." John rushed to explain, feeling as though he'd done something to be ashamed of. "You were begging me to stop." He frowned slightly. "To stop what, Sherlock? What was I doing?"

"Its nothing." Sherlock stated with a shaky sigh and he glanced over at the alarm clock, taking in the early hour. "Just go back to bed." John heard the crack in Sherlock's voice, noting how the tone had shifted higher than usual. Sherlock's right hand was absently playing with his curls. A sure sign that he was upset.

"Tell me." It wasn't an order, more of a suggestion. John wanted his friend to know that he was there for him.

"Its nothing." Sherlock repeated. "I'm fine." He tried to assure him but John didn't miss the flexing of his left hand against the bed sheets.

"Sherlock, please-"

"I don't want to talk about it, John." Sherlock interjected. He tried to be firm but was betrayed by a stray tear that forced its way down his cheek. John perched tentatively on the edge of Sherlock's mattress as he wiped away the teardrop.

"That's fine." John assured him with a soft smile. "If you don't want to talk about it then we don't have to. But I want you to know this;" He reached out, soothingly placing his hand on top of Sherlock's, "I would never hurt you. I would never purposely set out to hurt you physically, emotionally or mentally."

Sherlock continued to rub at his eyes, clearly trying to rid them of the tears. Once he was completely certain that his friend had stopped crying and was significantly calmer he stood from the bed, gathering Sherlock's pillows and handing them to him, allowing him to arrange them before carefully shifting his duvet and laying it over him.

"If you ever want to, or need to, talk at all, you know where I am. We could even text if that would make you more comfortable." John smiled before bidding him a goodnight and going to back to bed.

Thank you for reading.