Your Villain's Evil Plan will rely on many crimes being successfully committed. Listed below are many of the crimes your players may have in mind, and suggestions on how you can plan an evening around them.
The Break in
Breaking into a facility should be run like a one session dungeon crawl. The facility will be full of surprises, traps, monster lab experiments, and unexpected semi-super security guards. Good tools to use include a large map of the facility, and tokens representing the players characters in it. Pace the adventure so that it can be completed or failed in one game session.
Players will often need the assistance or leverage of powerful NPCs. Sometimes this assistance must be against their will, and this NPC will have to be kidnapped, manipulated, or interrogated. When running this type of game, prepare plenty of dialogue for the victim. Come up with a complete character profile and be prepared to improvise. While torture is unfortunately gruesome, it is not uncommon for villains. To preserve the light-hearted tone of the game, run torture as an off-camera type of event. Try keeping it to dice rolls and saving throws, and then take a short commercial break. Get a mountain Dew, or any other fine Pepsi product. Return to the game with the NPC either giving the data, or resisting, and make that the final word. The important thing to keep in mind at all times is to maintain the PG-13 rating. The comedy will be lost if the game gets too graphic.
Research and Development
A lot of R&D is necessary in the development and adaptation of devices and such. I recommend running a montage sequence, consisting of a lot of dice rolling, very quickly, and some loud music. Don’t make this take up too much game time, as it’s often exclusionary of some players, and is really just throwing plastic around and playing statistics. Choose a Villain's relevant stat, and have them roll. Count the number of times it takes for them to reach the goal, and make that the amount of time it will take to achieve their landmark. Play can then continue as normal, and this "R&D" can be considered to happen during the characters' time -off camera.
For example: Becky needs to learn how to modify a teleporter for an evil plan. She is rolling 1D6 every day she researches. the device is taken apart and put back together at a sum of 3, the device is understood at a sum of 10, the teleporter is improved at 14, and at 20 the teleporter can be programmed to create a vacuum, sucking all air and matter into a pocket dimension equivalent to an empty 150’ by 150’ x30’ warehouse.
The villains may be setting a trap for one or more NPCs. It is times like these that the GM has to remember they are working with, not against the players. The GM should consider the players' plan, how they intend the trap to work, and if it's important for the plan to fail, seed the group with the makings of their own failure. Plant suspicion, jealousy, and unique opportunities for revenge in such a way that the players self-sabotage. If after all of that they seem determined to let the plan succeed, be ready to treat them fairly and give them at least a partial success. If the NPCs escape a well crafted trap for no reason, it won't take long for the players to cry foul.
Sometimes the villains just want to hurt somebody. In these instances, be prepared to (through gameplay) remind the villains that they are the underdogs, and they don't stand a chance in a straight fight against Super High. Let them win their victories against security guards, scientists and police officers, but the moment they see a Super Hero, teach them to fear, and teach them to run.