You can get this after you take over the Smile Bakery as part of the story. Take the fast travel to the Smile Bakery and go east a screen. Go up to the "flour" on a piece of paper on the nearest table and you'll be thrown into a fight. They have a shit ton of HP (over 1 million) but I never saw them attack. Regardless a pestigenocide weapon or anything with instant kill is best for this. After a few turns the last one always ran away before I could kill it. After the fight ends you can do it again if you couldn't kill any of them.
The achievement unlocked the moment I killed one of them, so you don't even have to kill them all apparently.