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 ( Chandra ) , 54.0 ( XMM-Newton ) , and 66.9 ( Chandra ) after outburst . We confirm a \sim 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 \pm 267 km s ^ { -1 } on day 39.7 and of -771 \pm 65 km s ^ { -1 } 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 15 Å that originate from the radiatively cooling shock . On day 39.5 we find a systematic blue shift of -526 \pm 114 km s ^ { -1 } 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 1000 sec . 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 } .