Yeah, this is wild. Flash didn't do this, and just downloading a file doesn't magically change the system. Something obviously happened, but it's something low level that we would never have permission to touch in the first place.
First things first, when in doubt, reboot. Actually power the machine down. Give it ~30 seconds to let everything discharge. Restart it.
If that doesn't work, I can't tell what operating system I'm looking at, but boot into the relevant recovery mode and check the integrity of the disk and operating system. Most modern operating systems have a non-destructive repair option.
To give you any useful advice beyond that, I'm going to need to know more about your computer and browser. I'm happy to try and help (it's really weird and interesting), but we're way outside the scope of an actual Flash Player problem:
https://forums.adobe.com/thread/1195540