We present CRPropa 3.3, the latest release of the publicly available Monte Carlo framework for simulating the propagation of high-energy particles in astrophysical environments. This version introduces significant extensions that enables multi-messenger studies across a broad energy range, from GeV to ZeV. New features include explicit time tracking, time-dependent advection fields, and support for position-dependent radiation backgrounds, for more realistic simulations of Galactic and extragalactic propagation. Nuclear cross sections have been updated and expanded up to lead (Z=82). We illustrate some of these new features, including acceleration at moving shocks and gamma-ray propagation in the interstellar radiation field. Together, these improvements establish CRPropa 3.3 as a comprehensive tool for modelling cosmic rays, gamma rays, and their secondaries in structured, time-dependent environments, setting the stage for next-generation multi-messenger astrophysics.