CO oxidation over oxygen-rich Ru(0001) surfaces is one of the most studied catalytic oxidation reactions in surface science and of widespread interest as a model system for the redox chemistry of transition metal model catalysts. Here, we present an extensive low-energy electron microscopy (LEEM) and photoemission electron microscopy study of the oxidation of Ru(0001), which constitutes a crucial step in understanding the overall surface reaction. After characterizing the different surface nanoscale morphologies observed depending on the oxidation temperature, three distinct oxygen-rich phases are identified by dark-field microscopy and local valence-band spectroscopy. Furthermore, in situ LEEM allows us to follow the growth of single rutile oxide nuclei in real time and determine the relevant activation barriers that induce quasi-one-dimensional growth of oxide nanorods, whose growth rate is limited by O incorporation.