0o0o0o0o0o0o0o0o0o
Three clues.
First, there was the package. It contained a small cyllinder. Watson thought hard, and the last time he saw that little brass cylinder was at Sherlock's brother's house. His private store of oxygen.
The second thing was the question mark. He had left the typewriter, and he knew that when he stood that there was not a small, curved shape next to 'The End'.
And the last thing that tipped him off was a small dart. John thought back to a week ago, and when Sherlock had hidden himself with a suit that matched his background. He had shot at least three blow-darts at his friend.
Without another thought, the doctor rushed out of the room and up the stairs. He was no detective, but these three clues pointed him to the assumption, and perhaps, correct fact, that his best friend was alive.
0o0o0o0o0o0o0o0o0o
This might be a prequel to something, but for now it's just a one-shot.