In certain high power RF systems multipactor cannot be avoided for all operating points, but its existence places limits on performance, efficiency, lifetime, and reliability. As an example multipactor in the input couplers of superconducting RF cavities can be a major limitation to the maximum RF power. Several studies have concentrated on rectangular waveguide input couplers which are used in many light sources. Most of these studies neglect space charge assuming that the effect of space charge is simply to defocus the electron bunches. Modelling multipactor to saturation is of interest in determining the performance of waveguide under a range of conditions. Particle-in-cell modelling including space charge has been performed for 500 MHz half-height rectangular waveguide. Phase plots of electron trajectories can aid understanding the processes taking place in the multipactor. Results strongly suggest that the multipacting trajectories are strongly perturbed by space charge causing the electrons to transition from two-surface to single-surface trajectories as the multipactor approaches saturation.