The Yilgarn Craton (hereafter, the craton) is an archetypal Archean craton, with geology characterised by greenstone belts dating from ca. 3.7 Ga to ca. 2.7 Ga, separated by Neoarchean granite domains dating from 2.68 to 2.62 Ga. The isotopic record of crust forming events defines the growth of a geographically complete craton by the Neoarchean with stable crustal architecture prior to the intrusion of the Widgiemooltha Dolerite at 2.42 Ga. Geophysical studies of the lithospheric mantle resolve regionally variable Mg#: a highly depleted western craton (Mg# > 90.5) contrasts with a typically less depleted eastern craton (Mg# < 90.5), while the surrounding orogens and basins possess more fertile lithosphere (Mg# < 90.0). The lithospheric mantle composition for the eastern craton lies outside the range of xenolith data from Archean regions, suggesting post-Archean refertilisation. Refertilisation causes increased density associated with locally higher iron content as well as higher proportion of clinopyroxene and garnet, with respect to olivine and orthopyroxene. Over the large spatially-averaged volumes to which geophysical data are sensitive, distributed compositional variations generate detectable changes in bulk composition, while a horizontally-layered velocity structure at small scales, consistent with observations in peridotite massifs, may generate radial anisotropy in seismic wave propagation. As well as the cratons Archean geology, post-Archean igneous and sedimentary rocks record a prolonged lithospheric evolution that is not well resolved in datasets recording bulk crustal isotopic evolution. Reconciling these, we combine interpretation of geological and geophysical data to resolve two phases of lithosphere destabilisation driven by major magmatic events at ~2.06 Ga and at ~1.08 Ga. In the first stage we suggest that south-east directed mantle flow crosses a lithospheric step between the western and eastern craton, causing shear-induced edge-driven convection and associated sub-lithospheric melting and magmatism in the lee of this feature. The associated refertilisation is proposed to have generated ongoing subsidence and eastwards tilting over the subsequent ~250 Ma, with marine sediments deposited as the surface was drawn down through sea level. Late Mesoproterozoic tectonics led to the exposure of the north-eastern edge of the craton to instability, leading to basin forming and extensional brittle fracturing in the northern craton. We propose that, as the 1.08 Ga Giles Event impinged on this lithosphere, a subcrustal extrusion of fertile mantle emanated beneath the craton from a source region to the northeast. Extrusion of fertile mantle was accompanied by magmatism, emplacement of a crustal underplate and the thickening and refertilisation of the upper lithospheric mantle. The surface was elevated, supported by a thick and buoyant crust and hot mantle, however, as the lithospheric mantle cooled, subsidence led to the extensive sediment deposition over the north-eastern margin of the craton between 0.85 and 0.70 Ga. Magmatic destabilisation of the mantle and its recratonisation are key processes in craton evolution that are not always recognised in datasets recording crustal isotopic evolution. Such events can be detected through geophysical recognition of fertile mantle compositions, spatially associated with magmatic events, and the later formation of broad sedimentary basins over unrifted crust.