We provide a microscopic-level derivation of earlier results showing that, in the critical vicinity of the superconductor-to-insulator transition (SIT), disorder and localization become negligible and the structure of the emergent phases is determined by topological effects arising from the competition between two quantum orders, superconductivity and superinsulation. We find that, around the critical point, the ground state is a composite incompressible quantum fluid of Cooper pairs and vortices coexisting with an intertwined Wigner crystal for the excess (with respect to integer filling) excitations of the two types.