Declassified missions are an optional extra feature designed to make the game more challenging if you wish it to be. They are denoted by a large glowing crimson omen and if opted for will alter your experience in small ways, such as adding additional enemies or reducing your visibility. You can choose whether or not you'd like to activate them as you play through the game, but it is highly recommended you do because they allow you to earn Stars much quicker.
There is one declassified mission for each section of the campaign, NOT including Aftermath, for a grand total of 42. As their placement is not subtle at all, chances are you will run across at least one of them just playing through the game normally and will likely have this achievement fairly early on.
However, if not the very first declassified mission is in Chapter 1 Section 1. You can find the red symbol on the wall to your right immediately after fighting the first group of enemies near the flaming tree. Simply go near it, press the X button and then the A button to accept it. In this case, activating the declassified mission turns all the wretches you encounter into dark wretches instead. As soon as you finish the section, the achievement should pop.