The transition of the Franciscan Formation from accretionary wedge to continental crust is largely a consequence of processes within the slab window that develops in the wake of the Mendocino triple junction. Previously we have argued that the North American plate (Franciscan crust) was a relatively passive player in this process, but new geophysical and geodynamic modeling results point to a complex thermal and deformational history for both the Franciscan crust and slab window mantle. Rapid changes in crustal thickness coupled with a location for mantle inflow and melt generation south of the southern edge of the subducting Gorda slab, within the slab window produce a complex pattern of crustal melting, metamorphism and rheology that is reflected in the topographic evolution of the Coast Ranges, the location and style of volcanism, and the development of the superposed San Andreas fault system. Flow within the slab window produces a dynamic topography that is superimposed on the isostatic topography generated by the patterns of crustal and thermal structure. These results also imply that the thermal effects of MTJ passage and the opening of the slab window are focused south of the triple junction, more consistent with the location of active volcanisms and inferred lower crustal magma bodies. The source of mantle asthenosphere that fills the slab window (sub-slab, mantle wedge, sub-oceanic lithosphere, etc.) will determine not only the slab window’s thermal structure but also its chemical and rheologic characteristics. This can lead to differences in location, magnitude and chemistry of melts generated within the slab window, and the location and mechanical properties of the faults developed within the upper crust.