Molecular magnets based on heavy transition metals have recently attracted significant interest in the quest for novel magnetic properties. For systems with an odd number of valence electrons per molecule, high or low molecular spin states are typically expected in the double exchange or quasi-molecular orbital limits respectively. In this work, we use bulk characterization, muon spin relaxation, neutron diffraction, and inelastic neutron scattering to identify a rare intermediate spin-3/2 per dimer state in the 6H-perovskite Ba$_3$LaRu$_2$O$_9$ that cannot be understood in a double exchange or quasi-molecular orbital picture and instead arises from orbital-selective Mott insulating behavior at the molecular level. Our measurements are also indicative of collinear stripe magnetic order below $T_N$ = 26(1) K for these molecular spin-3/2 degrees-of-freedom, which is consistent with expectations for an ideal triangular lattice with significant next nearest neighbor in-plane exchange. Finally, we present neutron diffraction and Raman scattering data under applied pressure that reveal low-lying structural and spin state transitions at modest pressures P $le$ 1 GPa, which highlights the delicate balance between competing energy scales in this system.
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