The biggest mistake of Moriarty's career was to assume that John Watson was just a pet, a throw-away companion that Sherlock took on out of boredom or spite. He couldn't – or refused to – see that Dr. John Watson, MD, the studious jumper-clad former soldier who suffered from night terrors and hated Devon cream, was far more than a trifle: he was the heart to Sherlock's brains. He was the counterbalance to the consulting detective's tightly-bound madness, the coiled spring that put everything in action. He was what primed Sherlock for his sparks of genius, and the restraining force that protected Sherlock from spiraling out of control when he found himself trapped in his own intellect. Without John Watson, Moriarty would be out a nemesis. With John Watson, Moriarty would be in trouble indeed.
For the thing that both geniuses underestimated was John's incredible penchant for cold, calculated cruelty when he found it necessary. His strong moral compass served a higher purpose than the black-and-white reasoning of most other mundane men. John Watson was a soldier foremost, a doctor second, and he understood that sometimes to kill one was to save countless others. His conscience remained clean even after his most desperate murders, both in the war and after. And he knew he would sleep just fine tonight.
Moriarty would have spoken if he could. Maybe he would babble apologies, sneer, taunt John about his sheer ordinariness, how he could never sustain Sherlock's insatiable need for interesting, that ultimately the consulting detective would leave him for someone far more grandiose than he. But he couldn't. All that came out of his mouth were bloody bubbles and whimpers, the remnants of was once the whimsically named voicebox. His larynx was shredded, utterly destroyed by the jack knife John grabbed from the mantle in his fury.
"I am going to say it was self-defense," John said evenly, quietly. "You broke into our flat to try to steal some important documents. The note I sent you has been destroyed. There is no evidence to the contrary – I do live with the world's only consulting detective, after all. I've learned some tricks."
Moriarty's fading eyes made the figure before him wobble and blur until the cold blue eyes jumped into sharp focus, John bringing his face deafeningly close.
"I know what you were thinking. You thought I was useless. You thought that it was all Sherlock's doing, that everything up to now was just me playing along. Oh, no. You flatter yourself, Jim. You flatter yourself far too much." The doctor stood back, watching the man bleeding on his kitchen floor. Silently he thanked himself for shoving Moriarty against the fridge; the tile floor could be sprayed down without leaving stains. He didn't need another cleaning bill on his rent, and the wood floor in the living room was an original fixture. It would be a shame to have it ripped up because of an ignorant little sociopath.
Sirens wailed in the distance, responding to his emergency call. Yes, self-defense. John allowed himself a smile and glanced down at the man dying between his legs. "We all have our fatal flaws. Yours was underestimation."