To create a compelling plot for a villain crossover fanfic, start by thinking about what would bring these villains together. It could be a shared enemy that they initially don't realize they have until later in the story. As the plot progresses, show how their different personalities and methods of villainy either clash or complement each other. For example, if you have a cold - blooded, calculating villain like Hannibal Lecter teaming up with a chaotic and impulsive villain like Harley Quinn. The Lecter might be constantly trying to keep Harley in line while she's driving him crazy with her antics. And don't forget to have high - stakes consequences if they succeed or fail in their plans. This will keep the readers on the edge of their seats.
First, establish a common goal for the villains. It could be something like obtaining a powerful artifact that exists across multiple universes. Then, add conflict among the villains. Maybe one wants to use the artifact for personal gain while others have different motives. Also, introduce a hero or a group of heroes who are trying to stop them. This creates tension and a race for the villains to achieve their goal before the heroes interfere.