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A pick-pocket winds up dead at the police station from anthrax poisoning. Holmes and Watson investigate to find the source of the toxin. When it is discovered an anti-government group known as the Sovereign Army, they being to track down a man who has the motive. When he turns up dead after his brother shot him, it turns out that the brother was trying to kill off their herd of cows for $2.8 million.
Sherlock's close friend Alistair suddenly dies catches Holmes off guard. Holmes then begins to try to cope with the loss by acting out of character causing Joan to go into companion mode and making Sherlock talk about it. After it gets out the Alistair died of a heroine overdose, Sherlock struggles even more. Eventually, Homles confesses to Alistair at his grave that he loved him dearly and will miss him.