Getting the Villain Achievement requires you to complete all five levels of the first Villain Story, Riddler's Revenge, which follows the Riddler, Two-Face, Poison Ivy, Mr. Freeze, and Clayface.
In order to unlock Riddler's Revenge Villain Story, you must have completed the Hero Story first. Upon finishing that story (and getting the Hero Achievement) you will appear in the Batcave in front of a lever. Pull it to enter Arkham Asylum and be in control of Clayface and Riddler.
If you go to the left, you'll enter the mission room, and you will need to approach the bank van to start Riddler's Revenge.
Again, you must complete all five chapters, which are the events leading up to those played in the Hero versions of the Story. You will get this Achievement after completing the fifth Chapter as Riddler and Two-Face.
You will also unlock all the Villains from this Story in Freeplay after completing their respective level.