  We study the ionization and excitation structure of the interstellar medium
in the late-stage gas-rich galaxy merger NGC 6240 using a suite of emission
line maps at $\sim$25 pc resolution from the Hubble Space Telescope, Keck NIRC2
with Adaptive Optics, and ALMA. NGC 6240 hosts a superwind driven by intense
star formation and/or one or both of two active nuclei; the outflows produce
bubbles and filaments seen in shock tracers from warm molecular gas (H$_2$
2.12$\mu$m) to optical ionized gas ([O III], [N II], [S II], [O I]) and hot
plasma (Fe XXV). In the most distinct bubble, we see a clear shock front traced
by high [O III]/H$\beta$ and [O III]/[O I]. Cool molecular gas (CO(2-1)) is
only present near the base of the bubble, towards the nuclei launching the
outflow. We interpret the lack of molecular gas outside the bubble to mean that
the shock front is not responsible for dissociating molecular gas, and conclude
that the molecular clouds are partly shielded and either entrained briefly in
the outflow, or left undisturbed while the hot wind flows around them.
Elsewhere in the galaxy, shock-excited H$_2$ extends at least $\sim$4 kpc from
the nuclei, tracing molecular gas even warmer than that between the nuclei,
where the two galaxies' interstellar media are colliding. A ridgeline of high
[O III]/H$\beta$ emission along the eastern arm aligns with the south nucleus'
stellar disk minor axis; optical integral field spectroscopy from WiFeS
suggests this highly ionized gas is centered at systemic velocity and likely
photoionized by direct line-of-sight to the south AGN.
