The cathode for Lithium-ion batteries is dominated by transition metal oxides that exist in numerous polymorphic structures. To emphasize generality and the underpinnings of thermodynamics in the stability, activity, and kinetics of lithiation, we utilize the nomenclature of the native structure and non-native structure for referring to different transition metal oxides polymorphic structures. The native structure is the thermodynamic ground state (bulk phase) structure and various non-native structures have different discrete translational symmetry in their sub-surface regions compared to the native structure. Typically, non-native structures have higher (i.e. less negative) bulk formation energy and more open structures than the native structure. Hence, non-native structures are expected to generate higher discharge potential and better lithium mobility as a positive electrode material. However, non-native structures may be limited in stability, which can be increased by scaffolding them with the native structure. To explore these hypotheses, we synthesize pure Ramsdellite MnO2 (r/NN1-MnO2) and thermally phase transform it gradually to Pyrolusite MnO2 (β/N-MnO2) and intimately interfaced (r/NN1-MnO2)/(β/N-MnO2) intergrowth structures are obtained. As the temperature increases, the ratio of r/NN1-MnO2 to β/N-MnO2 in the intergrowth structure decreases; so does the discharge potential and lithium mobility in the lithium-ion coin cell. In addition, the galvanostatic discharge profile shows a wider discharge plateau for intergrowth structures as compared to the pure native and non-native structure. We rationalize these trends in discharge potential using formation energies computed via density functional theory followed by a statistical averaging to account for the different types of lithium intercalation sites in the intergrowth structures. The wider discharge plateau in the intergrowth structure is rationalized with the presence of additional interfacial sites of higher stability than the site available in single phase native and non-native structure. The capacity retention is higher for the intergrowth structure, which is ~64% compared to ~42% and ~32% as obtained for pure native and non-native structures after 100 cycles at a rate of 0.1C. The improved capacity retention for intergrowth structure is due to higher structural stability and available free volume, where the presence of native structure acts as a scaffold to stabilize the non-native structure. The electrochemical impedance spectroscopy suggests that the larger percentage of non-native structure helps in better transport due to greater free volume present in r/NN1-MnO2 structure with wider 2×1 channel compared to the native structure with the narrow 1×1 channel. This study demonstrates how a systematic control of the relative percentage of each phase, without change in chemical composition, helps in designing cathodes with improved capacity and cycle life, thereby expanding the available material space.