Neglected and abandoned heritage sites are a complex research topic, which always requires a thorough understanding of the site’s past and current condition. This article examines how research on history, architecture, and participation can contribute to creating a suitable re-use project for such heritage sites, focusing on a single case study: the Royal Citadel of Messina, Italy. Within the field of history, the city and fortification’s past underscores the importance of the site’s architectural and historical value. An urban analysis and documentation campaign were carried out during the field architecture. The urban analysis focused on the site as a remarkable natural landscape with industrial surroundings. The digital documentation, concentrating on the so-called cistern, emphasized the site’s values. Within a revalorization process, community participation is vital and is, therefore, one of the suggestions to consider in further developments. The last applied method is a comparative case study, namely, the submarine base at Saint-Nazaire, France. Considering the complexity and fragilities of the site, a framework is designed that provides suggestions for the conservation, revalorization, and re-use of the site of the Royal Citadel.