Graphene has been demonstrated to have unique properties not only in its virgin state but also by altering its environment through rotations in bilayer graphene, doping, and creating heterostructures with other 2D materials, which all lead to different functional behaviors. Another avenue to altering graphene is by using defects to generate p-orbital magnetism, which is of interest both to fundamental physics and potential application in new classes of spintronic devices. Indeed, atomic hydrogen creating sp3 defects attached to the graphene surface as well as vacancies in graphene have been shown to induce magnetism, while high energy (MeV) proton irradiation has been shown to produce ferromagnetism at room-temperature in graphite. However, detailed investigations of these systems are absent so that little is known about the density and configuration of defects, the role of interfaces, or how these relate to magnetism. In this thesis studies of single-layer graphene revealed that atomic deuteration indeed does lead to reversible chemisorption. However, it is found that atomic deuterium treatment of many-layer epitaxially grown graphene on C-face 4H-SiC (EG/SiC) only affects the surface graphene layer and the buried graphene/SiC interface. While this result did not present magnetism from the interface or graphene, x-ray reflectivity and cross-sectional transmission electron microscopy demonstrated a change of the buried graphene/SiC interface which resembles a delamination of graphene from the substrate. In some cases, multiple atomic treatments lead to complete delamination of the graphene film. Motivated by the results of atomic hydrogenation (deuteration), interlayer incorporation of hydrogen was achieved by accelerating ions to implant them between graphene sheets using low (100s of eV) energy hydrogen ion implantation. We focus on addressing the role of the damage from implantation in the magnetism which we observe in our samples. The use of polarized neutron reflectivity and x-ray scattering aims to uniquely address the relationship of strain, structural damage or chemisorption, and magnetism in many layer epitaxial graphene. We find that via tailoring the ion distribution (and range) to the sample we can reliably predict the structural and magnetic changes driven by implantation.