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I am going to be running a Heroes Unlimited/Ninja and Superspies Military Supers campaign. The Characters are 2 Military Intelligence and 1 grunt.
Their powers:

MI1: Alter Physical Structure: Smoke/mist and Meld with Weapons
MI2: Supernatural Strength, Unbreakable bones And Hardened Skin(Hair in his case, He is extremely Hairy) And continuing to mutate.
Grunt: Alter Physical Structure: Forcefield, Colorization and 1 other power I can remember.

What would be good missions to send these 3 on?

Create a superpowered terrorist group. Possibly focused of the destruction or subjegation of normal people.
Maybe send the on a covert mission in Bolivia to recon and assualt a major drug cartel leader. And have the cartel have a few super operatives of its own.
A superpowered mutant seizes control of a small third world country and attempts to put together a super army to start world war 3.
A spy steals a top secret power armor and the team has to track him or her down before he sells it to the highest bidder.

Just a few I thought of off the cuff. Hope they are helpfull.