The Allied Framework for Modeling and Simulation (M&S) as a Service (MSaaS) is proposed by NATO MSG-136 as a permanent service- and cloud-based M&S ecosystem for use by NATO and partner nations. The framework is designed to aid stakeholders to utilize state-of-the-art service-oriented and cloud-based methodology and technology to achieve interoperability between participating simulation systems and ensuring credibility of results. This paper presents the reference architecture that is currently developed as part of the technical concept for the Allied Framework for MSaaS. The reference architecture is structured on The Open Group SOA Reference Architecture, while its contents is supplied via the NATO C3 Taxonomy in the form of architecture building blocks and architecture patterns. The MSaaS Reference Architecture is not a final product. It will change over time as new architecture building blocks and patterns are identified and added, and existing ones modified and improved.