Process of Elimination

"Eliminate the impossible, John!"

John sighed heavily and looked down at his scattered notes. His conclusions were disjointed at best, frightening at the worst; the only positive side was that if a burglar or one of Mycroft's men decided to raid his flat, they likely wouldn't be able to decipher his handwriting.

Eliminate the impossible...

Very well. It was impossible for his friend to have committed suicide.

But he did.

Or did he?

"It's all a magic trick." John started as a sentence from that horrible last conversation invaded his conscience.

Then if he's not dead...

He must be alive.