Potential spoilers:
This IS a story related achievement, not exactly sure how far I am through the main campaign (roughly 60-70% I would say). You get this after you have 'collected' the three jokers and have done a "Dual takedown" on Harley Quinn. For this to happen, once you have beaten the three jokers (the lady, the fighter and Johnny Charisma), Henry Adams will call you saying that Harley Quinn is trying to get to him. Head over to the objective marker and some goons will be waiting on the other side of the gate. Now look for a grate on the ground (not the closest one to the gate but trace that tunnel back to the next grate around the corner). Hop in that grate and use the "voice synthesiser" and select a random guard and point at the button on the left wall. After this Harley will come out and a dialogue will ensue with Robin. Towards the end of the dialogue you can move Batman again, place him under the grate near Harley and wait until you get the "Dual takedown" symbol on your screen. Hit that and begin to fight the thugs and the achievement will pop!