The amalgamation of Gondwana and its subsequent fragmentation has been a subject of several studies over the past five decades, yet the very important question of the initial geometry of the supercontinent remains enigmatic. Current reconstruction models of the Indian Ocean are characterized by large gaps, overlaps and misfits of major structural and Cratonic bodies in their fit, and positions of tectonic blocks that are inconsistent with field observations, a phenomenon sustained by inadequate data, long standing debates and a lack of consensus on the nature of major structures and basins in the ocean. Past attempts to reconstruct the initial fit of the ocean has led to varied and complex models, with their own logic and different geographical limits, whose validity and underlying assumptions require testing in the light of current global geological and geophysical data. Our analysis of these models and their consequences on the continental passive margins brings to the fore critical scientific questions and the incoherencies that exist between them. This paper presents a compressive study of the structure of the Precambrian basement, Paleozoic marginal and rift basins of the plates constituting the Indian Ocean, examining the architecture and geochronological composition of their composing Cratons and crustal blocks, and delineating important structural markers to juxtapose them in full-fit reconstructions. We introduce a new holistic model from Gondwana’s initial geometry to Chron 34, achieved through a combination of onshore and offshore geological and geophysical data. Our new model is coherent with current data interpretations of major structures across the Indian Ocean. Consistent with the interpretation of the Beira High as continental crust, and recent seismic refraction interpretation of the Pamela MOZ3-5 expedition in the Northern Mozambique Ridge and Northern Natal Valley. The model also permits full extent of major cratonic, volcanic and sedimentary structures within the supercontinent, and presents a new synthesis upon which further work may be projected.