It has been proposed that the fullerene formation mechanism involves either a top-down or bottom-up pathway. Despite different starting points, both mechanisms approve that particular fullerenes or metallofullerenes are formed through a consecutive stepwise process involving Stone-Wales transformations (SWTs) and C2 losses or additions. However, the formation pathway has seldomly been defined at the atomic level due to the missing-link fullerenes. Herein, we present the isolation and crystallographic characterization of two isomeric clusterfullerenes Sc2O@C2v(3)-C78 and Sc2O@D3h(5)-C78, which are closely related via a single-step Stone-Wales (SW) transformation. More importantly, these novel Sc2O@C78 isomers represent the key links in a well-defined formation pathway for the majority of solvent-extractable clusterfullerenes Sc2O@C2n (n = 38-41), providing molecular structural evidence for the less confirmed fullerene formation mechanism. Furthermore, DFT calculations reveal a SWT with a notably low activation barrier for these Sc2O@C78 isomers, which may rationalize the established fullerene formation pathway. Additional characterizations demonstrate that these Sc2O@C78 isomers feature different energy bandgaps and electrochemical behaviors, indicating the impact of SW defects on the energetic and electrochemical characteristics of metallofullerenes.