Environmental issues play an increasingly important role in aviation, affecting the desirability of novel technologies directly. The desirability of a certain technology with respect to environmental issues is determined by the system of systems level impact instead of the often used system level impact. Changing this perspective introduces additional complexities in how the system level evaluation should be related to the desired system of systems (SoS) level evaluation. A framework is proposed, using agent based simulation, to evaluate the emergent behaviour of the intertwined stakeholders and the subsequent impact of the novel technology. The Maglev assisted aircraft launch system is considered as a test case to evaluate the complexities arising in the proposed approach. The three evaluated scenarios showed a large behavioural effect on the system of systems level environmental impact. Even though data in the scenarios were assumed and behaviour simplified, the knowledge obtained by the agent based simulation improved the understanding of the mechanisms affecting the environmental impact. Finally, the modular approach allows for an extension of the framework to evaluate more realistic scenarios.