Scalable and precise nanopatterning of graphene is an essential step for graphene-based device fabrication. Hydrogen-plasma reactions have been shown to narrow graphene only from the edges, or to selectively produce circular or hexagonal holes in the basal plane of graphene, but the underlying plasma-graphene chemistry is unknown. Here, we study the hydrogen-plasma etching of monolayer graphene supported on $\mathrm{Si}{\mathrm{O}}_{2}$ substrates across the range of plasma ion energies using scale-bridging molecular dynamics (MD) simulations based on reactive force-field potential. Our results uncover distinct etching mechanisms, operative within narrow ion energy windows, which fully explain the differing plasma-graphene reactions observed experimentally. Specific ion energy ranges are demonstrated for stable isotropic ($\ensuremath{\sim}2\phantom{\rule{0.28em}{0ex}}\mathrm{eV}$) versus anisotropic hole growth ($\ensuremath{\sim}20--30\phantom{\rule{0.28em}{0ex}}\mathrm{eV}$) within the basal plane of graphene, as well as for pure edge etching of graphene ($\ensuremath{\sim}1\phantom{\rule{0.28em}{0ex}}\mathrm{eV}$). Understanding the complex plasma-graphene chemistry opens up a means for controlled patterning of graphene nanostructures.