Pelagic organisms' movement and motion of buoyant particles are driven by processes operating across multiple, spatial and temporal scales. We developed a probabilistic, multi-scale model, the Connectivity Modeling System (CMS), to gain a mechanistic understanding of dispersion and migration processes in the ocean. The model couples offline a new nested-grid technique to a stochastic Lagrangian framework where individual variability is introduced by drawing particles' attributes at random from specified probability distributions of traits. This allows 1) to track seamlessly a large number of both actively swimming and inertial particles over multiple, independent ocean model domains and 2) to generate ensemble forecasts or hindcasts of the particles' three dimensional trajectories, dispersal kernels, and transition probability matrices used for connectivity estimates. In addition, CMS provides Lagrangian descriptions of oceanic phenomena (advection, dispersion, retention) and can be used in a broad range of oceanographic applications, from the fate of pollutants to the pathways of water masses in the global ocean. Here we describe the CMS modular system where particle behavior can be augmented with specific features, and a parallel module implementation simplifies data management and CPU intensive computations associated with solving for the tracking of millions of active particles. Some novel features include on-the-fly data access of operational hydrodynamic models, individual particle variability and inertial motion, and multi-nesting capabilities to optimize resolution. We demonstrate the performance of the interpolation algorithm by testing accuracy in tracing the flow stream lines in both time and space and the efficacy of probabilistic modeling in evaluating the bio-physical coupling against empirical data. Finally, following recommended practices for the development of community models, we provide an open source code with a series of coupled standalone, optional modules detailed in a user's guide.