Described are systems and methods for evaluating cyber effects in a cyber-physical system (CPS). In some embodiments, a simulation model of the CPS is built and includes an attacked component set and an evaluated component set. A control component is inserted into the simulation model. One or more direct connections between the attacked component set and the evaluated component set are disconnected. One or more indirect connections are identified and then disconnected from the simulation model with disconnected direct connections. The one or more direct connections and indirect connections are routed through the control component. A cyber-attack on the attacked component set can be simulated by configuring the control component to control outputs transmitted via a routed connection, the routed connection being one of the routed direct or indirect connections. The simulated components of the simulation model can be progressively and iteratively replaced by corresponding components from the CPS.