How was the whole crime planned, and who is the murderer of the story?

There is a great deal of deception in this work, starting with Porlock and Moriarty. The central deception, of course, is John Douglas, who is actually McMurdo, who is actually Birdy Edwards. Edwards deceives all of the Scowrers as well as Ettie initially; then in England he deceives Cecil and his wife. The deception deepens with his faked death, but even then it is not enough to fool Moriarty (or Holmes, of course). Deception is used for both moral and immoral reasons. Moriarty deceives to gain power; Edwards deceives in order to gain access to a society of murderers whom he seeks to bring down. Doyle suggests that deception may be useful but that one has to be very careful to not lose himself within the disguise.

Douglas is not murdered, he fakes his death, deceiving his friends and his enemies to bring down the Scrowrers while undercover.