I. FIGURE CAPTIONS Fig. 1 (a) ˜ A-B Bernal stacking structure for bilayer graphene. (b) C$_{Hol}$ system, where the atom in violet is the foreign C atom. (c) N$_{Bri}$ system, where the atom in blue is the foreign N atom. (d) O$_{Bri}$ system, where the atom in red is the foreign O atom. Fig. 2 Side-view of charge contours for C$_{Bri}$, N$_{Bri}$ and O$_{Bri}$ systems, respectively. Fig. 3 Electronic and magnetic structures of the C$_{Hol}$ system. (a) Band structure of ma- jority spin, (b) band structure of minority spin, (c) total density of states, (d)the orbital-resolved DOS for the foreign C atom, (e) density of states for spin unpolarized C$_{Hol}$ system, (f) distribution of the spin density on the lower graphene layer.. Fig. 4 Spin-resolved band structure and density of states of N$_{Bri}$ system. (a) Band structure of the majority spin; (b) band structure of the minority spin, (c) total density of states, (d) partial density of states of N atom. Fig. 5 Band structure and density of states of O$_{Bri}$ system. (a) Band structure, (b) total density of states, (c) partial density of states of O atom. Table I The binding energy ( dE ), the length of bonding between the adsorption atom and its nearest C atom ( a$_{C-atom}$ ), and the bilayer distance of the adsorption system ( dis. ). The stable position for each intercalated atom is noted by box. Table II The stable positions for adsorption atoms C, N, and O in monolayer and bilayer graphene. 9