Initially, the villain seems to have one goal but the hero later finds out that the villain has a far more sinister, evil goal with horrifying consequences.
In the beginning of “Star Wars,” Darth Vader just appears to want to capture Princess Leia. Later we learn that he wants to capture her because she had the stolen Death Star plans. Finally, we learn what Darth Vader really wants, which is to blow up the rebel base using the Death Star.
In the beginning of “Die Hard,” the villain initially appears to be nothing more than a terrorist holding a corporate Christmas party hostage. Only later do we gradually learn the villain’s real goal, which is to steal corporate bonds and blow up the hostages on the roof to create a distraction so they can escape.
In “WALL-E,” the villain initially appears relatively harmless. Only later do we learn that the villain is trying to destroy a plant that WALL-E found. Then we learn that the real reason the villain wants to destroy this plant is to keep the human race marooned in space forever.
Think of the villain in any good story and he or she likely has a vague or minor goal. However, that vague or minor goal is really part of something much larger and more evil.
What ties the hero and villain together is their mutual pursuit of a Symbol of Hope. The hero needs this Symbol of Hope to achieve an emotional dream while the villain needs the same Symbol of Hope to achieve an evil goal. Because both the hero and villain need the Symbol of Hope and only one can have it, they must fight each other until only one can have it.
The best stories don’t reveal the villain’s true intentions right away. Instead, they create a mystery over what the villain wants. In some cases, the villain may even appear to be a friend of the hero such as the villain in “Ghost,” who secretly hired someone to rob the hero.
However, as the story progresses, we must gradually see that the villain’s initial actions are far from harmless. Instead, these actions are part of a much larger pursuit of a totally evil goal.
So give your villain an ulterior motive. At first the villain may not appear so bad but that’s because we don’t know the real story, and that real story is that the villain really is evil after all.