All cells are covered in little bumps called antigens. Your body contains antibodies that bind to antigens on foreign cells. Your white blood cells then only attack cells that have antibodies attached to them.
So it’s not about good/bad, but really just about which cells are your own and which are foreign.
Usually, autoimmune diseases fuck it all up.
It has lots of false positives and false negatives. It is actually a very simplistic system, if it was “smart enough” we wouldn’t have diseases. In fact, a good number of diseases, especially chronic ones that millions or billions of people suffer from throughout their lives, are actually the immune system’s fault. It is not a “smart” system. It is clever. Sometimes. Until it’s not.
Your own cells have protein signature directly dependent on the genetics. Everything that doesn’t match is attacked