The Molopo Farms Complex is an extremely poorly exposed, major, ultramafic-mafic layered intrusion straddling the southern border of Botswana with South Africa. It lies within the south-western part of the ~2.0 Ga large igneous province of southern and central Africa that includes the better known Bushveld Complex. Integrated interpretation of regional gravity data and new high-resolution airborne magnetic data have constrained the geometry of the Molopo Farms Complex in southern Botswana as a strongly faulted, polyphase intrusion compartmentalised by regional ductile shear zones. Previous models showing that the Complex was emplaced in at least two discrete stages are supported. Ultramafic rocks were initially emplaced as a semi-coherent lopolithic sheet up to about 4 km in thickness cutting across Transvaal Supergroup strata that had already been folded into open eastwest trending dome and basin structures with wavelengths of about 4 km. Steeply dipping, dyke-like ultramafic bodies adjacent to, and within major shears are inferred to be solidified feeders to the main lopolithic part of the MFC. It is likely that the initial ultramafic sheet was emplaced at a high crustal level (<3 km depth) into an attenuated Transvaal Supergroup sequence. This lack of a thick hanging wall sequence is thought to be significant for the emplacement of the succeeding mafic sheets. The ultramafic sheet thermally altered its wall rock and also created a complex fracture system in its hanging wall rocks. Differentiation within the ultramafic sheet produced basal harzburgites overlain by bronzites and possibly mafic sheets. Later mafic/basic sheets and dykes, again fed along shear-controlled, steeply dipping zones, spread into the fracture network created by the initial emplacement of the ultramafic lopolith to form a distinctive spider’s-web pattern on high-resolution airborne magnetic maps. It is proposed that either post-emplacement regional folding or gravitational collapse of the basal ultramafic lopolith produced a major basin with a ~40 km eastwest diameter, north of the Jwaneng-Makopong Shear Zone and smaller basin to the southeast. The newly postulated, steeply dipping ultramafic/mafic feeders, as well as the ultramafic lopolith and areas with anomalous nickel values in soils are considered to be prospective for PGE-bearing magmatic nickel-copper sulphide mineralisation. Magmatic rocks dated at about 2.0 Ga are a common feature, not only of the Kaapvaal Craton, but of all the African cratonic blocks south of the Equator. Reactivated intracratonic faults and shears appear to control emplacement of individual magmatic complexes although a sub-continental thermal anomaly unconfined by lithospheric plate boundaries is a likely driving force for the widespread magmatism.