Rutherford devised an experiment where alpha particles were fired at a very thin sheet of gold leaf. His detectors were at first place behind the foil and a large number of protons were detected as flashes of light on the detector. Slowly they were brought to the side of the foil and still his staff were detecting protons. He then placed the detector beside the proton 'gun' and very occasionally detected a particle. His hunch had paid off. He likened this event as 'firing a 7 inch shell at a piece of tissue paper and it coming straight back'.
What he had found was the Nucleus of an atom of gold. The positively charged proton had met with the positively charged nucleus of the gold atom and it had been rebounded due to like charges repelling . Looking at his data he reasoned that the Nucleus was surrounded by a relatively large void before the electron cloud was encountered. He likened the relative size of the atomic nucleus to the distance to the electrons as the 'fly in the cathedral'. Neils Bohr went on to further refine this model.