I just played coop for an hour and 15 minutes trying to beat my first mission on dark agent. keep in mind that i havent unlocked the dark agent mode yet. finally i beat it and im like why didnt i get the achievement. so i go to missions and it shows just 3 stars there. Im wondering, did the dark agent count? As in, will it count that i did it after i beat all of the missions on perfect agent on coop?

the only way to find out is to try, i have heard of the same problem you are having, that you cant get the achievement unless youve unlocked it first