Generating pores in graphene by decoupled nucleation and expansion is desired to achieve a fine control over the porosity, and is desired to advance several applications. Herein, epoxidation is introduced, which is the formation of nanosized epoxy clusters on the graphitic lattice as nucleation sites without forming pores. In situ gasification of clusters inside a transmission electron microscope shows that pores are generated precisely at the site of the clusters by surpassing an energy barrier of 1.3 eV. Binding energy predictions using ab initio calculations combined with the cluster nucleation theory reveal the structure of the epoxy clusters and indicate that the critical cluster is an epoxy dimer. Finally, it is shown that the cluster gasification can be manipulated to form A-scale pores which then effectively sieve gas molecules based on their size. This decoupled cluster nucleation and pore formation will likely pave the way for an independent control of pore size and density.