We use a 2.5D hybrid simulation to study the breathing mode (BM) dynamics in Hall thrusters (HTs). This involves a 1D Euler fluid simulation for neutral dynamics in the axial direction, coupled with a 2D axial–azimuthal Particle-in-Cell (PIC) simulation for charged species. The simulation also includes an out-of-plane virtual dimension for wall losses. This setup allows us to replicate the BM’s macroscopic features observed in experiments. A comprehensive analysis of plasma parameters in BM’s phases divides it into two growth and two decay sub-phases. Examining 1D axial profiles of electron temperature, gas and plasma densities, and particle creation rate shows that an increase in electron temperature alone cannot sustain ionization. Ionization seems to be influenced by the spatial correlation between electron and gas densities and the ionization rate coefficient. Investigating ion back-flow reveals its impact on modulating neutral flux entering the ionization region. The hybrid simulation’s outcomes let us assess the usual 0D predator–prey model’s validity and identify its limitations. The ionization and ion convection term approximations hold, but the gas convective term approximation does not. Introducing an alternative gas convective term approximation involving constant density ejection from the ionization region constructs an unstable BM model consistent with simulation results. In addition, this paper explores how varying the imposed voltage and mass flow rate impacts the BM. The BM frequency increases with imposed voltage, aligning with theoretical predictions. The mass flow rate variation has a limited effect on BM frequency, following the theoretical model’s trend.