The motion of interfaces is an essential feature of microstructure evolution in crystalline materials. While atomic-scale descriptions provide mechanistic clarity, continuum descriptions are important for understanding microstructural evolution and upon which microscopic features it depends. We develop a microstructure evolution simulation approach that is linked to the underlying microscopic mechanisms of interface migration. We extend the continuum approach describing the disconnection-mediated motion of interfaces introduced in Part I [Han, Srolovitz and Salvalaglio, 2021] to a diffuse interface, phase-field model suitable for large-scale microstructure evolution. A broad range of numerical simulations showcases the capability of the method and the influence of microscopic interface migration mechanisms on microstructure evolution. These include, in particular, the effects of stress and its coupling to interface migration which arises from disconnections, showing how this leads to important differences from classical microstructure evolution represented by mean curvature flow.