Hello, Scotty!
I own a Mercedes c200 w203 2.2L diesel and I have removed the catalytic converter and also installed a EGR emulator in order to turn off the EGR valve and stop the black smoke coming out of my car. After a month or two the Check Engine light started flashing and I had it checked by a mechanic, he said it's something about emissions. I do not own an OBD2 scanner or anything. What should I do in order to get rid of it?

you removed the emissions system, the computer knows that. You can't fix it unless you put back on the stuff you took off and fix it.