There was a reason Doctor John Watson was an army doctor. He had the courage of any soldier. He had a cool head and an intrinsic compassion for people. He hated to see suffering, but had waded into the middle of a war to help people. If they were alright, his own comfort didn't matter.
When John met Sherlock, that compassion was tested, almost on a daily basis. He found Sherlock to be abrasive and rude, and the way he treated poor Molly. It was like living with a twelve year old! It took a little while for him to trust this strange, compelling man. John knows when he trusted him completely, though. Sherlock had rid him of his psychosomatic limp. He didn't get looks of pity or sympathy anymore. He'd been restored.
So when hare-brained Sherlock dragged him along on a case, he didn't protest. He missed it. He was bowled over by Sherlock's amazing capacity for knowledge and his keen observations. He was equally bowled over by his almost total disregard for humanity at times; all that mattered was the case.
John Watson had called Sherlock Holmes a machine once. He was wrong. Sherlock was his best friend. He was the person John would risk his life for, because Sherlock had given him his life back.
When John had a bomb strapped to him, he didn't flinch. His soldier instincts kicked in and he kept his cool. They almost died that night, both of them. It was pure chance Moriarty was distracted enough to allow them to live.
When John was in that lab with a ferocious hound lusting for his blood, he called Sherlock. He was terrified of dying alone. He begged, tears in his eyes, for his friend to get him out of there. Everything went bright and Sherlock's bright eyes were there in front of him and everything was alright again. The fury and hurt and utter fear John felt when Sherlock revealed it was an experiement… he thought if it was someone else, if it wasn't his best friend, he might have killed him.
Ultimately, his best friend killed him. He watched him jump. He watched as his best friend announced he was a fraud, that he'd lied, that he'd researched him- but of course, John Hamish Watson never believed a word that came out of his mouth. He believed in his friend, his comrade.
He was in denial for the whole funeral. He kept thinking he'd turn to his side and Sherlock would be there, alive and healthy. Instead, there was Lestrade, who he could see had be crying from the tracks on his cheeks- God he was getting like Sherlock- and Mrs Hudson, looking shrunken by his side. And finally Molly, unusually tear-free and stony faced. She left pretty quickly… it must have been hard for her.
Later, when he was alone, he stood at Sherlock's graveside. There was something of the man in the stone; black and unyielding. He never did remember the moment he began to sob, sinking to his knees.
'Come back. God, Sherlock, just come back. This is enough. Nobody is going to kill us. Just come back.'
He doesn't remember the exact moment he was no longer alone.
'Shh. John, it's okay. Shh.'
It was Molly. She knelt beside him, cradling him like a child as he cried for his best friend, the most human human being he knew. He could have sworn the words 'he's alive,' ghosted past her lips.
Doctor John Hamish Watson, Afghanistan war veteran, friend, brother (and occasionally) boyfriend was a soldier. He was going to get through it. So he grieved. He grieved for the lost friend who was still very much alive and hiding out in Molly Hooper's flat. He got over his best friend. He finally had a stable relationship. He'd asked her to marry him. She'd said yes.
When Sherlock knocked on their door three years afterward, the first thing John did was floor him with a great punch to the face, putting all his strength behind it. Sherlock had anticipated this reaction, so he took the beating without complaint. The second thing was to crush him in a gigantic bear hug.
Sherlock was the best man at John's wedding. He finally saw his best friend happy. He owed him that much. He owed John so much. His best friend. His comrade. Doctor John Watson.