Fuzzy Cognitive Maps (FCMs) were developed as a tool for capturing and modelling the behaviour of qualitative system dynamics. However, several drawbacks have been identified that limit FCMs ability in simulating the behaviour of qualitative system. This paper addresses the limitations of FCMs in modelling complex qualitative system dynamics and proposes a generalised Fuzzy Cognitive Mapping (FCM) approach that is able to overcome those limitations. This approach uses fuzzy rules to represent the dynamics of concepts and relations, including time dynamics of relations and introduces a multistep simulation approach that can use several single layer perceptrons to simulate the dynamics of concepts and relations overtime. This approach also incorporates the fuzziness and ambiguity widely associated with expert knowledge when representing and simulating the dynamics of concepts and relations. In this paper, the design of the proposed generalised FCM approach is explained and demonstrated for a real-world case of the consequences of high intensity rainfall in Kampala City, Uganda. This generalised FCM approach creates a new perspective and an alternative approach to model the behaviour of complex qualitative system dynamics using FCMs.