We present a multiphase analysis of the gas in the circumnuclear region (∼0.9 × 0.9 kpc2) of the nearby barred Seyfert 1.8 galaxy NGC 1365, observed as part of the Mid-IR Activity of Circumnuclear Line Emission (MIRACLE) program. Specifically, we combined spatially resolved spectroscopic data from JWST/MIRI, VLT/MUSE, and ALMA to provide a multiphase characterization of the ionized atomic and the warm and cold molecular gas phases. MIRI data enabled the detection of more than 40 mid-IR emission lines from ionized or warm molecular gas. Moment maps show that both cold and warm molecular gas trace the circumnuclear ring, following the rotation of the stellar disk. The ionized gas exhibits flux distributions and kinematics that vary depending on the ionization potential (IP). Low-IP species (≤25 eV) mainly trace the rotating disk, while higher-IP species (up to ∼120 eV) trace the outflowing gas. Both [O III] λ5007 Å and [Ne V] λ14 μm trace the nuclear outflow cone toward the southeast. In addition, the [Ne V] λ14 μm line traces the counter-cone of the outflow to the northwest, which is obscured in the optical at these circumnuclear scales, and is thus undetected in [O III] λ5007 Å. Unlike optical diagnostics, spatially resolved mid-IR diagnostics reveal the key role of the active galactic nucleus (AGN) as the source of gas ionization in the central region. We derived the electron density from the [Ne V] λ24 μm/[Ne V] λ14 μm line ratio, finding a median value of (750 ± 440) cm−3, consistent with previous estimates obtained from the optical [S II] doublet. Lastly, we applied, for the first time, a fully self-consistent combination of state-of-the-art photoionization and kinematic models (HOMERUN + MOKA3D) to estimate the intrinsic physical outflow properties, kinematics, and energetics ─ overcoming the limitations of classical methods based on oversimplified assumptions. Exploiting the unprecedented synergy between JWST/MIRI and VLT/MUSE, HOMERUN allows us to simultaneously reproduce the fluxes of over 60 emission lines spanning from the optical to the mid-IR. This unique approach enables us to disentangle the physical conditions of AGN- and star formation-dominated components and robustly estimate the mass of the outflowing gas and other physical properties.