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Ca₂RuO₄ is a correlated transition metal oxide that exhibits a Mott transition (IMT) concurrent with a symmetry preserving Jahn-Teller distortion (JT) at 350 K. This strong coupling between the electronic and structural transitions in Ca₂RuO₄ makes studying the role played by individual degrees of freedom nontrivial. Since the Mott insulating state relies on a half-filled band, it is instructive to use optical photo-excitation to disrupt orbital ordering and the associated Mott State without directly perturbing the crystal structure. Using spectroscopic measurements with sub-picosecond temporal resolution and nano-scale spatial resolution, we interrogate the interplay and level of codependency of the JT and IMT via thermal cycling through the transition and electron-hole injection. Through the thermodynamic pathway, we observe phase coexistence in the form of a stripe phase existing at the domain wall between bulk insulating and metallic regions. Through the ultrafast carrier injection pathway, we observe the formation of localized mid-gap states that lead to enhanced absorption in the time domain with no spatial inhomogeneity. We posit that these mid-gap states become localized via polaronic features related to the local perturbation of the JT distortion.