Heteroatom-doped metal-free graphene has been widely studied as the catalyst for the oxygen reduction reaction (ORR). Depending on the preparation method and the dopants, the ORR activity varies ranging from a two-electron to a four-electron pathway. The different literature reports are difficult to correlate due to the large variances. However, due to the potential metal contamination, the origin of the ORR activity from “metal-free” graphene remains confusing and inconclusive. Here we decipher the ORR catalytic activities of diverse architectures on graphene derived from reduced graphene oxide. High angle annular dark field scanning transmission electron microscopy, X-ray absorption near edge structure, extended X-ray absorption fine structure, and trace elemental analysis methods are employed. The mechanistic origin of ORR activity is associated with the trace manganese content and reaches its highest performance at an onset potential of 0.94 V when manganese exists as a mononuclear-centered structure within defective graphene. This study exposes the deceptive role of trace metal in formerly thought to be metal-free graphene materials. It also provides insight into the design of better-performing catalyst for ORR by underscoring the coordination chemistry possible for future single-atom catalyst materials.