Ion irradiation has been observed to induce a macroscopic flattening and in-plane shrinkage of graphene sheets without a complete loss of crystallinity. Electron diffraction studies performed during simultaneous in-situ ion irradiation have allowed identification of the fluence at which the graphene sheet loses long-range order. This approach has facilitated complementary ex-situ investigations, allowing the first atomic resolution scanning transmission electron microscopy images of ion-irradiation induced graphene defect structures together with quantitative analysis of defect densities using Raman spectroscopy.