The urgent need for research and study with nondestructive and noninvasive methods and the preservation of cultural heritage led to the development and application of methodologies for the multi-level digitization of cultural elements. Photogrammetry and three-dimensional scanning offer photorealistic and accurate digital representations, while X-rays and computed tomography reveal properties and characteristics of the internal and invisible structure of objects. However, the investigation of and access to these datasets are, in several cases, limited due to the increased computing resources and the special knowledge required for their processing and analysis. The evolution of immersive technologies and the creative industry of video games offers unique user experiences. Game engines are the ideal platform to host the development of easy-to-use applications that combine heterogeneous data while simultaneously integrating immersive and emerging technologies. This article seeks to shed light on how heterogeneous digital representations of 3D imaging and tomography can be harmoniously combined in a virtual space and, through simple interactions, provide holistic knowledge and enhanced experience to end users. This research builds on previous experience concerning the virtual museum for the Antikythera Mechanism and describes a conceptual framework for the design and development of an affordable and easy-to-use display tool for combined representations of heterogeneous datasets in the virtual space. Our solution was validated by 62 users who participated in tests and evaluations. The results show that the proposed methodology met its objectives. Apart from cultural heritage, the specific methodology could be easily extended and adapted for training purposes in a wide field of application, such as in education, health, engineering, industry, and more.