  The pyrochlore ruthenate In$_2$Ru$_2$O$_7$ displays a subtle competition
between spin-orbital entanglement and molecular orbital formation. At room
temperature, a spin-orbit-entangled singlet state was identified. With
decreasing temperature, In$_2$Ru$_2$O$_7$ undergoes multiple structural
transitions and eventually forms a nonmagnetic ground state with semi-isolated
Ru$_2$O units on the pyrochlore lattice. The dominant hopping through the
Ru-O-Ru linkage leads to molecular orbital formation within the Ru$_2$O units.
This molecular orbital formation is unique in that it involves the O$^{2-}$
anions, unlike the transition-metal dimers observed in systems with
edge-sharing octahedra. We argue that the covalent character of In-O bonds
plays a pivotal role in the structural transitions and molecular orbital
formation and such bonding character of "$A$-site" ions is an important
ingredient for electronic phase competition in complex transition metal oxides.
