Military airdrop is the best suggestion IMO. My idea for a hard mission is that you would have to go to a specific outpost or bunker to get a piece of military-grade hacking software, then go to another specific outpost or bunker and hack into a terminal there to bring an outpost back online for the army. This would be difficult as a result of these bunkers/outposts being especially heavily guarded.
Something else that crossed my mind as I typed this up is the idea of making USBs actually useful by having specific buildings in specific cites (with consoles, of course) be “secured” by downloading software on a USB port and using the port on the console in said building. Applicable buildings could include yet more bunkers and outposts and perhaps office towers and offices.
Just my two cents on the matter (although by the time you’re reading this inflation has probably halved the worth of two cents).