The phase of Super-Soft-Source (SSS) emission of the sixth recorded outburst of the recurrent nova RS Oph was observed twice with Chandra and once with XMM-Newton. The observations were taken on days 39.7, 54.0, and 66.9 after outburst. We confirm a 35-sec period on day 54.0 and found that it originates from the SSS emission and not from the shock. We discus the bound-free absorption by neutral elements in the line of sight, resonance absorption lines plus self-absorbed emission line components, collisionally excited emission lines from the shock, He-like intersystem lines, and spectral changes during an episode of high-amplitude variability. We find a decrease of the oxygen K-shell absorption edge that can be explained by photoionization of oxygen. The absorption component has average velocities of -1286+-267 km/s on day 39.7 and of -771+-65 km/s on day 66.9. The wavelengths of the emission line components are consistent with their rest wavelengths as confirmed by measurements of non-self absorbed He-like intersystem lines. We have evidence that these lines originate from the shock rather than the outer layers of the outflow and may be photoexcited in addition to collisional excitations. We found collisionally excited emission lines that are fading at wavelengths shorter than 15A that originate from the radiatively cooling shock. On day 39.5 we find a systematic blue shift of -526+-114 km/s from these lines. We found anomalous He-like f/i ratios which indicates either high densities or significant UV radiation near the plasma where the emission lines are formed. During the phase of strong variability the spectral hardness light curve overlies the total light curve when shifted by 1000sec. This can be explained by photoionization of neutral oxygen in the line of sight if the densities of order 10^{10}-10^{11} cm^{-3}.
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