This will not help you make a super villain. But it will help you figure out what they're trying to accomplish. Roll once on each table.
What they're going to do to the target (1d6)
 Replace with fake copy/Sabotage to have an 'accident'
 Steal/Gain control of
 Hijack/Capture (and use as leverage for huge ransom)
 Experiment on/Research
 Politically manipulate/slander local leaders about
Who they Sent (1d10)
 Low powered super henchmen and 2d6 lackeys
 1d6 lackeys who hired 3d6 street gang members for backup.
 1d6 lackeys with 1d8 flying battledroids for backup
 3 Extremely strong, mutant, humanoid animals. Breaking their collars frees them of control.
 1d6 naked super men. Don't use weapons, can punch through steel and deflect bullets.
 Hypnotized local politician/rich celebrity, using leverage instead of direct force.
 2d6 highly trained tacticool mercenaries
 Sprung 1d4 super villains from jail party defeated before. May have learned new tricks.
 2d6 lackeys with a fucking tank, helicopter, or submarine.
 If you want something done right, you've got to do it yourself.
Secret Weapon to make sure plan succeeds (1d12)
 Skin-tight bio suit grants regeneration and fast reflexes. Given to the 'leader' of each squad.
 Villain has hacked nearby security cameras and is transmitting footage to minions.
 Schoolbus full of kids for hostages.
 Sniper mercenary, in a tower over a mile away. Never misses a shot.
 Hologram technology. Super Villain appears there but is not.
 One of those sent has the weakness of one of the super heroes up his sleeve.
 Experimental stomping war mech. Has a stupid mechanical oversight, like can't go backwards.
 One family member or love interest of a random super hero on the team.
 One of those sent is a blanker. Can temporarily neutralize the powers of one random super hero.
 Local police have been paid off or distracted, can't help at all.
 Blocks easy transport; super heroes won't be able to get there in time if they take normal route.
 Experimental laser guns given to each minion. If they hit a reflective surface the gun explodes.
And the Target (1d50)
 First self-aware AI robot
 Great 'first wave' super hero, in stasis inside a cyropod
 Experimental Cure for incurable disease
 Nuclear missile in decommissioned silo
 Last remaining tissue samples of thwarted alien invaders from a few decades ago
 Hyper advanced prosthetic. Works better then flesh and blood.
 Secret recipe of global fast food chain.
 The Terrafloppy disk- holds all internet data in physical form in case of massive server wipe.
 Hydro-electric dam; provides power to millions, breaking it will cause massive flood.
 Airplane with experimental weather control device mounted on it.
 Area 51
 Corporate office, contains trillions of dollars worth of classified data.
 Source code for government security systems. Could shut down a whole region's mega-shield.
 The only zombie. It's bite could still infect people.
 Hyper-car, police could never catch it. Bright neon lights and doors that go up.
 Prop from a beloved classic movie.
 All of the “Best in Show” dogs from the past 15 years.
 Innocent young teenage girl who can read minds. Not a super hero or villain yet.
 The DNA of the most evil super villain of all time.
 Magic 'indestructible' knight armor from middle ages.
 Magic red candle. If lit and bible is read backwards, opens portal to hell.
 Molecule assembler. Can mass produce anything, like gold or anthrax.
 Elevator to Earth's core.
 The almost completed space elevator.
 The only sample of Unobtainium 12 on Earth.
 Dinosaur DNA, trapped in amber.
 First brain uploader. Anyone uploaded to the internet could bypass any security.
 Time-Paradox baby clone of one of the super heroes. Could be molded to evil.
 Super acid. Can melt through anything except special container with squirt nozzle.
 CIA registry of every super heroes secret identity.
 Shrink ray.
 Ultra rare marble quarry. Rich people make floors with it.
 Power booster. Extends range of any super power to a mile OR doubles its effect.
 Invisibility material, whatever it covers is invisible. Enough to make a single body suit.
 Portal to alternate dimension where super powers never happened.
 Statue of selfless super hero who sacrificed themselves to save the city.
 Island resort hotel.
 The president's sex toys. Locked in special discrete briefcase.
 Ancient tablet containing records of the world's first ever language.
 Fishing vessel. It caught the real Loch Ness monster.
 Secret documents of massive conspiracy. Moon landing faked, holocaust never happened, etc.
 Genetically modified, elephant sized pig. Has like a hundred blue ribbons.
 The preserved brain of a super scientist. Could invent almost anything.
 Perpetual motion machine.
 Gallon jug of super fuel. Could blow up a city, or power a rocket ship to light speed.
 Scroll of an Egyptian philosopher. The meaning of life is written on it.
 The lost city of Atlantis.
 Unreleased episode of an old cartoon. Watching it makes people kill themselves.
 Controls to secret rocket thrusters put on the moon.
 Golden telephone. If you wait on hold for one hour you can talk to God on the other end.