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Of course M is alive, and he is the 3rd sibling mentioned in passing in Vow. He is Sherlock's fraternal twin, given over to an institution within 2 years of birth due to psychotic behavior. Mycroft judged all children as idiots from his childhood experience with M and the "stupid" Sherlock, who wanted to grow up to be a pirate. M came out of nowhere because he liberated himself from the asylum as soon as he was capable.
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I wonder if Moriarty, or someone affiliated with him, was able to look enough like Sherlock that he could impersonate Sherlock in the final scene and frame Sherlock for a killing? We know Moriarty WOULD do that - he's done it once before - and if he's alive he must be pretty upset that both Sherlock and Sherlock's reputation survived the first time.
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Assuming that M was aware of the actions of Mi-6, it is quite possible that he waited to let the justice system eliminate his foe before going public. He went public several minutes before Sherlock's reprieve.