Solid state joining of titanium via friction stir welding and diffusion bonding have emerged as enablers of efficient monolithic structural designs by the eliminations fasteners for the aerospace industry. As design complexity and service demands increase, the need for joints of dissimilar alloys has emerged. Complex thermomechanical conditions in friction stir weld joints and high temperature deformation behavior differences between alloys used in dissimilar joints gives rise to a highly variable flow pattern within a stir zone. Experiments performed welding Ti-6Al-4V to ß21S show that mechanical intermixing of the two alloys is the primary mechanism for the generation of the localized chemistry and microstructure, the magnitude of which can be directly related to pin rotation and travel speed weld parameters. Mechanical mixing of the two alloys is heavily influenced by strain rate softening phenomena, and can be used to manipulate weld nugget structure by switching which alloy is subjected to the advancing side of the pin. Turbulent mixing of a weld nugget and a significant reduction in defects and weld forces are observed when the ß21S is put on the advancing side of the weld where higher strain rates are present. Chemical diffusion driven by the heat of weld parameters is characterized using energy dispersive x-ray spectroscopy (EDS) and is shown to be a secondary process responsible for generating short-range chemical gradients that lead to a gradient of alpha particle structures. Diffusion calculations are inconsistent with an assumption of steady-state diffusion and show that material interfaces in the weld nugget evolve through the break-down of turbulent interface features generated by material flows. A high degree of recrystallization is seen throughout the welds, with unique, hybrid chemistry grains that are generated at material interfaces in the weld nugget that help to unify the crystal structure of dissimilar alloys. The degree of recrystallization is tied to the localized thermal profile in the weld nugget as well as the heating rates of a given set of weld parameters. Slow kinetics of alpha dissolution relative to the heating rate and process times of friction stir welding suggest an alpha-particle assisted super-transus recrystallization process contributes to a refined grain size in weld parameters utilizing high travel speed.