In this paperwe describe CO2-PENS, a comprehensive system-level computational model for performance assessment of geologic sequestration of CO2. CO2-PENS is designed to perform probabilistic simulations of CO2 capture, transport, and injection in different geologic reservoirs. Additionally, the long-term fate of CO2 injected in geologic formations, including possible migration out of the target reservoir, is simulated. The simulations sample from probability distributions for each uncertain parameter, leading to estimates of global uncertainty that accumulate through coupling of processes as the simulation time advances. Each underlying process in the system-level model is built as a module that can be modified as the simulation tool evolves toward more complex problems. This approach is essential in coupling processes that are governed by different sets of equations operating at different time-scales. We first explain the basic formulation of the system level model, briefly discuss the suite of process-level modules that are linked to the system level, and finally give an in-depth example that describes the system level coupling between an injection module and an economic module. The example shows how physics-based calculations of the number of wells required to inject a given amount of CO2 and estimates of plume size can impact long-term sequestration costs.