We have used a new, isentropic-coordinate three-dimensional chemical transport model to investigate the decay of ClO and evolution of other species in the Antarctic polar vortex during September 1992. The model simulations cover the same southern hemisphere period studied in a companion data paper by Santee et al. [this issue]. The model is initialized using the available data from the Microwave Limb Sounder (MLS) and Cryogenic Limb Array Etalon Spectrometer (CLAES) on the Upper Atmosphere Research Satellite (UARS). During the model initialization chemical inconsistencies in the UARS data became evident. Fields of odd nitrogen (NOy) derived from CLAES N2O underestimated the sum of the direct observations of the major NOy species. Results from the model integrations at 465 K and 585 K are sampled in the same way as the various UARS instruments and compared to the observations both directly and by considering average quantities in the inner and edge vortex regions. Sampling the observed species in the same way as the UARS instruments is important in removing any spurious trends due, for example, to changing solar zenith angle. While the model can reproduce the magnitude of the MLS ClO observations at 585 K, this is not possible at 465 K. The model partitions too much ClO into Cl2O2 to reproduce the observed ClO which is around 2.0 parts per billion by volume (ppbv) averaged within the polar vortex. The model also underestimates CLAES ClONO2 in the inner vortex at 465 K due to heterogeneous processing. The observations require that effectively all of the inorganic chlorine is in the form of ClO and ClONO2 in the inner vortex at this altitude. In the basic model run, the decay of ClO produces ClONO2 which is not observed by CLAES. Our results indicate the potential importance of the speculative reaction between OH and ClO producing HCl for the recovery of HCl in the Antarctic spring. By including this reaction, the decay of model ClO into HCl is enhanced, yielding better agreement with HCl data from the Halogen Occultation Experiment (HALOE) data. Similar results can also be obtained by including the reaction between HO2 and ClO to produce HCl with a 3% channel. The model generally reproduces the observed O3 destruction during September. The most significant discrepancy for O3 is in the inner vortex at 465 K where the model underestimates the observed O3 loss rate, especially when the effects of vertical motion are included.