The findings herein complement our previous report of simultaneous nanopore filling and intercalation during the low-voltage plateau region, with pore sizes that preferentially fill depending on microstructure as determined from operando SAXS and XAS measurements. Finally, we differentiate sodium insertion between graphene layers via adsorption at intralayer defects from the conventional intercalation mechanism in which sodium adsorbs at the high symmetry points between graphene layers. We suggest that the comprehensive mechanism we propose for sodium storage in HC microstructures is generalizable and should be tested across different precursors and synthesis conditions to confirm its broader applicability.