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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.