Markarian 6 is a nearby (D~78 Mpc) Seyfert 1.5, early-type galaxy, with a double set of radio bubbles. The outer set spans ~7.5 kpc and is expanding into the halo regions of the host galaxy. We present an analysis of our new Chandra observation, together with archival XMM-Newton data, to look for evidence of emission from shocked gas around the external radio bubbles, both from spatially resolved regions in Chandra and from spectral analysis of the XMM data. We also look for evidence of a variable absorbing column along our line of sight to Mrk 6, to explain the evident differences seen in the AGN spectra from the various, non-contemporaneous, observations. We find that the variable absorption hypothesis explains the differences between the Chandra and XMM spectra, with the Chandra spectrum being heavily absorbed. The intrinsic N_H varies from ~8x10^{21} atoms*cm^{-2} to ~3x10^{23} atoms*cm^{-2} on short timescales (2-6 years). The past evolution of the source suggests this is probably caused by a clump of gas close to the central AGN, passing in front of us at the moment of the observation. Shells of thermal X-ray emission are detected around the radio bubbles, with a temperature of ~0.9 keV. We estimate a temperature of ~0.2 keV for the external medium using luminosity constraints from our Chandra image. We analyse these results using the Rankine-Hugoniot shock jump conditions, and obtain a Mach number of ~3.9, compatible with a scenario in which the gas in the shells is inducing a strong shock in the surrounding ISM. This could be the third clear detection of strong shocks produced by a radio-powerful Seyfert galaxy. These results are compatible with previous findings on Centaurus A and NGC 3801, supporting a picture in which these AGN-driven outflows play an important role in the environment and evolution of the host galaxy.
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