Source/drain formation in ultra-thin body devices by conventional ion implantation is analyzed using atomistic simulation. Dopant retention is dramatically reduced by backscattering for low-energy and low-tilt angles, and by transmission for high angles. For the first time, molecular dynamics and kinetic Monte Carlo simulations, encompassing the entire Si body, are applied in order to predict damage during implant and subsequent recovery during anneal. These show that amorphization should be avoided as recrystallization in ultra-thin-body Si leads to twin boundary defects and poly-crystalline Si formation, despite the presence of a mono-crystalline Si seed. Rapid dissolution of end-of range defects in thin-body Si, caused by surface proximity, does not significantly reduce diffusion lengths. The conclusions of the atomistic modeling are verified by a novel characterization methodology and electrical analysis.