This is a story related achievement and cannot be missed, so don't worry, if you finish the game you will get it eventually.
Spoilers:
There are a lot of drones to deal with, but your ally can help you as long as you stay near his / her fortress. Shouldn't be a hard fight, just play safe, use the batmobile weapons when they are charged and try to hit the drones' weak points when you can for an easy kill.