Abstract-The self-consistent time-dependent code MAGY is presently being used for designing and modeling gyrodevices. In this paper, the code's self-consistent capability is used to investigate three different issues relating to the operation of gyroklystron amplifiers. These are the effect of window reflection on the properties of the output waves, higher order mode excitation in nonlinear output tapers, and excitation in cutoff drift sections. The first two effects can potentially have major impacts on the gyroklystron output radio frequency (RF) in terms of bandwidth power ripple, phase ripple across the band, and mode purity. In fact, strong correlation between simulation results and experimental data indicates that the observed bandwidth ripple in a recently tested W-band gyroklystron can be attributed to a small (-20-dB) window reflection. The last effect, excitation in cutoff drift sections, is found to result in a high level of RF fields at the drive frequency in drift sections. This effect impacts the design and use of lossy ceramics in the drift section because of thermal considerations, particularly in high average power devices.