In this, the villains did something to the hero so that the heroine had to rescue him. And then at the end of the story, the hero had to blast the villains' stronghold (with the heroine's help).
Notice that this describes neither the villains' purpose nor their motives for it. . . there's a lot of possibilities.
poke, poke, poke Going to be something scientific and chemical and controlling. It fits thematically.
Now, if I could only figure out the villains for another story, where the heroine received a magical lantern and key ring. Something more specific than their taking prisoners -- that being obvious.