While most did pass through, Rutherford was shocked to find that:
To look inside the atom, Rutherford needed to fire something at it. He used: Rutherford Gold Foil Experiment - Backstage Science
At the time, scientists believed in the , where an atom was a blob of positive charge with electrons scattered inside like fruit in a pudding. If this were true, the heavy alpha particles should have whizzed straight through the "soft" atoms. While most did pass through, Rutherford was shocked