This article presents analytical and simulation studies of intense heavy ion beam propagation, including the injection, acceleration, transport and compression phases, and beam transport and focusing in background plasma in the target chamber. Analytical theory and simulations that support the High Current Experiment (HCX), the Neutralized Transport Experiment (NTX), and the advanced injector development program, are being used to provide a basic understanding of the nonlinear beam dynamics and collective processes, and to develop design concepts for the next-step Integrated Beam Experiment (IBX), an Integrated Research Experiment (IRE), and a heavy ion fusion driver. Three-dimensional nonlinear perturbative simulations have been applied to collective instabilities driven by beam temperature anisotropy, and to two-stream interactions between the beam ions and any unwanted background electrons; three-dimensional particle-in-cell simulations of the 2-MV electrostatic quadrupole (ESQ) injector have clarified the influence of pulse rise time; analytical studies and simulations of the drift compression process have been carried out; syntheses of a four-dimensional particle distribution function from phase-space projections have been developed; and studies of the generation and trapping of stray electrons in the beam self-fields have been performed. Particle-in-cell simulations, involving preformed plasma, are being used to study the influence of charge and current neutralization on the focusing of the ion beam in NTX and in a fusion chamber.