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We have detected faint \ha\ emission from several points along the Magellanic Stream, using the Rutgers Fabry--Perot Interferometer at the CTIO 1.5-m telescope. The sources of the emission are diffuse; at each surveyed position, there is little variation in intensity over the 7\arcmin\ field of the Fabry--Perot. At points on the leading edges of H~I concentrations within the clouds MS II, MS III, and MS IV, we detect emission with surface brightness ranging from 0.2 to 0.5 Rayleighs (1~R = $10^6 / 4\pi$~photons~\cmsqssr), or EM of 0.7 to 2 cm$^{-6}$ pc. In each field the \ha\ velocity agrees with the 21~cm velocity. We have surveyed several positions near the MS IV concentration, and find that the strongest emission is on the sharp leading-edge density gradient. The emission decreases at points away from the gradient, and halfway between MS III and MS IV the \ha\ surface brightness is down to $\lesssim 0.03$~R.
We interpret this correlation of \ha\ intensity with cloud leading edges as caused by shocks, as the material of the Stream collides with an ambient medium of ionized gas in the halo of the Galaxy. These observations suggest that ram pressure from halo gas plays the dominant role in stripping the Stream out of the Magellanic Clouds. The observed \ha\ flux implies the presence of relatively large amounts of gas -- $n_{\rm H} \sim 10^{-3}~\rm{cm}^{-3}$ -- in the Galactic halo at large radius, 40 to 50 kpc, and far above the Galactic plane, at $b = -70\deg$ to $-90\deg$. Such large coronal gas densities are difficult to reconcile with X-ray and cooling timescale constraints if the gas is a smooth ionized halo, but may be compatible with a lower-density ionized halo which contains a population of partially-ionized clouds with low column-density H~I. This accords well with models of Lyman-$\alpha$ and metal-line quasar absorption lines in which the absorption systems are resident in extended galactic halos.
