The California Institute of Technology (CIT) three-dimensional urban/regional atmospheric model is used to perform comprehensive gas- and aerosol-phase simulations of the 8 September 1993 smog episode in the South Coast Air Basin of California (SoCAB) using the atmospheric chemical mechanism of part 1 <Griffin et al., 2002> and the thermodynamic module of part 2 <Pun et al., 2002>. This paper focuses primarily on simulations of secondary organic aerosol (SOA) and determination of the species and processes that lead to this SOA. Meteorological data and a gas and particulate emissions inventory for this episode were supplied directly by the South Coast Air Quality Management District. A summer 1993 atmospheric sampling campaign provides data against which the performance of the model is evaluated. Predictions indicate that SOA formation in the SoCAB is dominated by partitioning of hydrophobic secondary products of the oxidation of anthropogenic organics. The biogenic contribution to total SOA increases in the more rural eastern portions of the region, as does the fraction of hydrophilic SOA, the latter reflecting the increasing degree of oxidation of SOA species with atmospheric residence time.