In the autumn of 2021, the Swedish Defence Research Agency was awarded a research grant from the Swedish Transport Administration for a pilot study on transport systems in crises and war. The pilot study had three principal goals: the development of a knowledge base, the formation of an interest group, and the development of an application for a research programme. This report presents the knowledge base and proposes the establishment of a research programme with the overarching purpose to understand how preparedness can be integrated into the development and planning of transport systems. The report discusses how transportation can be understood as a system-of-systems consisting of three independent though connected system levels: the infrastructural level, the transport operational level and the logistical level. Important differences between these levels, for instance in time perspectives and involved actors, are examined. The report examines existing scenarios for future transport systems as well as for possible threats against these. It concludes that a research programme needs to develop further scenarios for future transport systems, while it could base its threat scenarios on existing scenarios. The impact of technological development need to be integrated into the scenarios. In order to analyze how preparedness can be integrated in the regional and national planning processes for transport systems, crisis management, and civil defense, the understanding of how these processes function must be developed.