Molecular dynamics and quasidynamics simulations, utilizing the Tersoff many-body potential, were used to investigate projectile incorporation and defect production as well as lattice relaxation, diffusion, and annihilation of defects resulting from 50 eV Si irradiation of (2×1)-terminated Si(001). A unity trapping probability, in sites distributed between the epitaxial overlayer and the fourth lattice layer (l=4), was obtained for Si projectiles irradiating an array of high- and low-symmetry points in the primitive surface unit cell. Exchange epitaxy events were observed in which a lattice atom came to rest at an epitaxial (1×1) bridge site while the projectile stopped in a substitutional lattice site. In addition, several collision sequences resulted in the opening of additional dimers, up to four per irradiation event, thus providing (1×1) sites for migrating adatoms during ion-assisted crystal growth. The primary residual lattice defects produced were split and hexagonal interstitials, although tetragonal, bond-centered, and pentagonal interstitials were also produced in layers l=2 through l=14 with the average interstitial layer depth <l≳=2.3. Calculated interstitial migration activation energies Em decreased toward the surface with minimum energy paths generally involving tetragonal sites. Ion-irradiation-induced interstitials can thus be easily annealed out over time periods corresponding to the deposition of less than one monolayer under typical Si molecular-beam-epitaxy conditions. Fewer vacancies were produced, although they have a higher migration activation energy, and they were distributed over a shallower depth, l≤7. Complete annealing of ion-irradiation-induced vacancies requires interaction with deeper interstitials, moving toward the surface, and incident Si projectiles.