In Rutherford’s experiment three things happened:
- some alpha particles that were deflected
- some alpha particles came back at him
- some alpha particles went straight through the gold foil.
The particles that completely went through passed through the empty space in the atom. The particles that were deflected to the sides were deflated by a passing electron that moved the alpha particle out of the way. The particles that were bounced back hit the nucleus in the center that it bounced off.