1999 Saturn Sedan Transmission Bumping and Black Transmissi

Transmission problem
1999 Saturn Sedan Automatic 111000 miles

Hi there, I am not very car saavy, so pardon my ignorance on the issue.
About 5 months ago, I bought a '99 Saturn Sedan that now has about 111,000 miles on it. I've noticed that it would occasionally bump while accelerating and one night, on a particularly long drive, it began doing it very frequently. It had never done it more than once a trip and now it was going every couple minutes or so. Some of the shifting bumps were a little more aggressive than others, too.
I took it to the shop immediately and they checked my transmission fluid to found it full, but it was black. THe guy mentioned something like my car was having trouble "seeing through all the oil" so it was "upping the pressure." I don't know what he meant, sorry!
A transmission flush was suggested, but I've heard it can make the situation a billion times worse by loosening built-up gunk and getting things clogged.
Should I just empty and replace the fluid?
Should I go with the flush?
Should I go with a flush and a filter change?

Thanks for all your help!