Increasing ship emissions are of big concern because they contribute to the effects of climate change and have an impact on the local and regional environment. Due to these concerns, stricter regulations are enforced upon the shipping sector by the International Maritime Organisation and the European Union. However, since new regulations are enforced, stakeholders have been slow to react. A key reason why investment decisions are not taking place is that of uncertainty in regulations and policy. Besides, the availability of bunker infrastructure in ports is key to the development of alternative fuels. The objective of this study is to obtain insight into what possible future scenarios of the deployment of alternative fuels for the short sea shipping might arise and to provide insight into the effects of collaborative port strategies on the emergence of alternative fuels European maritime short sea sector taking into account regulatory and technological uncertainties. By means of an agent-based modelling approach and exploratory modelling and analysis approach, the influence of these uncertainties and policies is addressed. This enables to obtain a better understanding of where the system might go. The findings of this study show the effect of regulation enforcement and the need for a well-developed methanol bunker infrastructure across Europe to enable the transition to alternative fuels.