Using X-ray photoemission microscopy, we discovered that oxidation of commercial large-scale graphene on Cu foil, which typically has bilayer islands, by atomic oxygen proceeds with the formation of the specific structures: though relatively mobile epoxy groups are generated uniformly across the surface of single-layer graphene, their concentration is significantly lower for bilayer islands. More oxidized species like carbonyl and lactones are preferably located at the centers of these bilayer islands. Such structures are randomly distributed over the surface with a mean density of about 3 x 106 cm(-2) in our case. Using a set of advanced spectromicroscopy instruments including Raman microscopy, X-ray photoelectron spectroscopy (mu-XPS), Auger electron spectroscopy (nano-AES), and angle-resolved photoelectron spectroscopy (mu-ARPES), we found that the centers of the bilayer islands where the second layer nucleates have a high defect concentration and serve as the active sites for deep oxidation. This information can be potentially useful in developing lateral heterostructures for electronics and optoelectronics based on graphene/graphene oxide heterojunctions