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This achievement, as well as "The Royal Protector," is story-related and cannot be missed provided you choose to play as Emily during Mission 1, A Long Day in Dunwall.

In regards to gameplay, Corvo and Emily differ slightly in the powers they are given by The Outsider (provided you accept his gift/mark during the second mission of the game). Other than their different supernatural powers, mechanically, they play similarly. It's worth noting that character interactions will differ over the course of your playthrough depending on who you choose, but it does not impact the overarching narrative in any significant way.

All in all, choosing Corvo and completing the game as the masked assassin will yield "The Royal Protector," while completing the game as Emily will unlock "The Empress."