We present a pilot study of the z=2.923 radio galaxy MRC0943-242, where we for the first time combine information from ALMA and MUSE data cubes. Even with modest integration times, we disentangle an AGN and a starburst dominated set of components. These data reveal a highly complex morphology, as the AGN, starburst, and molecular gas components show up as widely separated sources in dust continuum, optical continuum and CO line emission observations. CO(1-0) and CO(8-7) line emission suggest that there is a molecular gas reservoir offset from both the dust and the optical continuum that is located ~90kpc from the AGN. The UV line emission has a complex structure in emission and absorption. The line emission is mostly due to i) a large scale ionisation cone energised by the AGN, ii) a Ly-alpha emitting bridge of gas between the radio galaxy and a heavily star-forming set of components. Strangely, the ionisation cone has no Ly-alpha emission. We find this is due to an optically thick layer of neutral gas with unity covering fraction spread out over a region of at least ~100kpc from the AGN. Other, less thick absorption components are associated with Ly-alpha emitting gas within a few tens of kpc from the radio galaxy and are connected by a bridge of emission. We speculate that this linear structure of dust, Ly-alpha and CO emission, and the redshifted absorption seen in the circum-nuclear region may represent an accretion flow feeding gas into this massive AGN host galaxy.