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Remote sensing of the nighttime OI 135.6\ nm emissions has been a widely used method for measuring the\ F\ region ionospheric plasma densities. In this work, we first develop a comprehensive radiative transfer model from first principles to investigate the effects of different physical processes on the production and transport of the 135.6\ nm photons in the ionosphere and then propose a new approach for estimating electron densities from the nightglow. The forward modeling investigation indicates that under certain conditions mutual neutralization can contribute up to \~38\% of the total production of the nighttime 135.6\ nm emissions. Moreover, depending on the ionospheric conditions, resonant scattering by atomic oxygen and pure absorption by oxygen molecules can reduce the limb brightness observed by satellite-borne instruments by up to \~40\% while enhancing the brightness viewing in the nadir direction by typically \~25\%. Further analysis shows that without properly addressing these effects in the inversion process, the peak electron density in the\ F\ region (NmF2) obtained using limb observations can be overestimated by up to \~24\%. For accurate estimation of the ionospheric electron density, we develop a new type of inverse model that accounts for the effects of mutual neutralization, resonant scattering, and pure absorption. This inversion method requires the knowledge of O and O₂\ densities in order to solve the radiative transfer equations. Application of the inverse model to the nighttime ionosphere in the noiseless cases demonstrates that the electron density can be accurately quantified with only \~1\% error in NmF2 and hmF2.