The nuclei of atoms become unstable when the repelling forces of the protons cannot be balanced by the number of neutrons in the nucleus. It then re-arranges itself randomly to a more stable configuration by emitting any of a series of particles. During radioactive decay, an atom does not collapse.
Since an atom is mostly empty space - that is it’s nucleus is relatively distant from the electron shells so, in the presence of extreme forces such as gravity inthe collapse of a large star, the inward pressures on the atom overcome the natural balance of the atomic structure and the ‘empty space’ disappears as nuclei are mashed together by the intense pressures and a neutron star is formed. Under even more external pressure, even the neutron star can collapse to form a black hole.