John woke up the next morning terrified. He wasn't sure how much Sherlock knew about his nightmares, and that alone was enough to make him wish it was still the night before.
But gradually, slowly, over weeks and months, he learned to stop being afraid. John Watson found out that Sherlock knew not to press further when John said he needed time alone, and that Sherlock actually did have his best interests at heart. Later on, Sherlock found out what it was that worried John so much. It would take a long time before John wouldn't jump at the sight of his best friend with a knife, but the two of them found how to work around it.
John found himself returning to work, and being less overwhelmed than it made him felt when he was still having nightmares. Sherlock waited before asking him on a case again. The first one they did go on together was small, with no dead bodies. And, even though Sherlock wasn't always the most affectionate person, he would often hug John when he looked as if he needed it.
There were always going to be late nights where John found himself wondering if his friend still cared, or why. No matter how hard Sherlock tried to, he couldn't stop it. He did, however, make them just that bit more bearable.