The scientific objective of SAFOD is to understand the physical and chemical processes of deformation and earthquake generation within an active, plate-bounding fault. Comprehensive understanding will be possible only if the structure and geochemistry of the fault zone are thoroughly documented and integrated with other data. This collaborative effort will characterize the composition, structure and deformation mechanisms of the San Andreas fault at the Observatory. Observations of core and cuttings from the pilot hole and first two phases of drilling (2004-2005), and of samples from fault exposures near the drill site, will be integrated with geophysical and hydrologic data presented in other SAFOD studies to address key questions regarding structure, physical properties and mechanics of the fault, and to test hypotheses of earthquake rupture dynamics, energy balance, and fault weakening. Work includes determining fault rock lithology, and distributions and orientations of fractures, secondary faults, veins, and particle sizes, and targeting key structures for detailed microstructure, mineralogy, and geochemistry analyses.