The intercalation of heteroatoms between graphene and a metal substrate has been studied intensively over the past few years, due to its effect on the graphene properties, and as a method to create vertical heterostructures. Various intercalation processes have been reported with different combinations of heteroatoms and substrates. Here we study Si intercalation between graphene and Ru(0001). We elucidate the role of cooperative interactions between heteroatoms, graphene, and substrate. By combining scanning tunneling microscopy with density functional theory, the intercalation process is confirmed to consist of four key steps, involving creation of defects, migration of heteroatoms, self-repairing of graphene, and growth of an intercalated monolayer. Both theory and experiments indicate that this mechanism applies also to other combinations of hetero-atoms and substrates.