Sherlock woke to the sound of a scream.
The scream was of average length, coming from downstairs tending to the left of their flat. It was a male's voice. Primary emotion was fear, not anger. It was John's voice, he realised.
Sherlock had processed that information in a decent length of time, accounting for the disorientation from waking suddenly. He spared another moment to scan his bedroom for a weapon; best to be prepared.
The bedside lamp was the only viable option, and with some struggle, he hefted it over his head. Mrs Hudson's furnishings left a lot to be desired when it came to makeshift weaponry.

"John?" he asked, the lamp held aloft as he searched through the flat. John's bed was in a state of distress, the sheets tangled and with a substantial amount of sweat on them.
"Are you alright?" Sherlock hissed into the near darkness, leaving the empty bedroom. "Fine," John's voice came from the kitchen, almost perfectly level. Sherlock let down the lamp, feeling foolish and went to the kitchen.

"I thought perhaps you were being attacked," Sherlock said, and noticed John's bleary eyes, and slight marks in his palms where he had dug in his nails into them.
"Yes, sorry about that," John replied unhelpfully, pouring himself a glass of water and then heading back to his room.
Sherlock turned back to his own when John called out, "Will you be wanting your lamp back then?"
"Ah yes, the lamp. Goodnight John."
"'Night."

Sherlock was not fooled. John had clearly had had a particularly strong nightmare. He spent several moments contemplating what could have provoked it, but John had asked him to stop analysing him anyway, and Sherlock let it be.
Well, almost. He took simple precautions the next morning; he moved John's gun from the bottom sock drawer, and put the fake lighter one that Sherlock had taken from the cabbie in its place. The decoy would not fool John in daylight, but Sherlock hoped that if he had another nightmare or simply got confused, then it would be enough to fool him, and then no one would get accidentally hurt.

It was the following night, when John shouted again that Sherlock realised what had caused it, and was ashamed he hadn't understood earlier.
It was the pool incident. Of course John of all people, would have issues with having a bomb strapped to him.
Sherlock softly walked into the sitting room, and seated himself in his chair, and waited there in the darkness, just to make sure.