Though YB6 and LaB6 share the same crystal structure, atomic valence electron configuration, and phonon modes, they exhibit drastically different phonon-mediated superconductivity. YB6 superconducts below 8.4 K, giving it the second-highest critical temperature of known borides. LaB6 does not superconduct until near-absolute zero temperatures, however. Though previous studies have quantified the canonical superconductivity descriptors of YB6’s greater Fermi-level (Ef) density of states and higher electron-phonon coupling (EPC), the root of this difference has not been assessed with full detail of the electronic structure. Through chemical bonding, we determine low-lying, unoccupied 4f atomic orbitals in lanthanum to be the key difference between these superconductors. These orbitals, which are not accessible in YB6, hybridize with pi B-B bonds and bring this pi-system lower in energy than the sigma B-B bonds otherwise at Ef. This inversion of bands is crucial: the phonon modes we show responsible for superconductivity cause the sigma-orbitals of YB6 to change drastically in overlap, but couple weakly to the pi-orbitals of LaB6. These phonons in YB6 even access an electronic-state crossing, indicating strong EPC. No such crossing in LaB6 is observed. Finally, a supercell (the M k-point) is shown to undergo a Peierls-like effect in YB6, introducing additional EPC.