We study the behavior of a number of siderophile elements, including platinum-group elements, during the formation of the Medek dunite–wehrlite intrusion. Its structural position, internal structure, and mineralogical composition are presented; a 3D geochemical model is constructed. The forsterite content of olivine varies from 90 to 73% from top to bottom of the vertical cross section of the intrusion. In addition, there is a decrease in the volume content of olivine and the appearance of ilmenite instead of accessory Cr-spinel. The observed zonation in variations in the composition of rocks and minerals is consistent with magmatic differentiation in a sheet-like body, which changed its primary occurrence. A geodynamic scenario is proposed, which links the formation of the intrusion with the break-up of Rodinia and the further changes in the primary occurrence with subsequent accretion–collision events on the southern and southwestern margins of the Siberian craton in the period 600–450 Ma.