In this Letter, we investigate the nature of the dramatic ‘superbubble’ emission structures associated with the z= 2.44 radio galaxy MRC 0406−244, using rest-frame optical spectroscopy and an archival Hubble Space Telescope (HST) Near-Infrared Camera and Multi-Object Spectrometer (NICMOS) image. Based on the optical line ratios and the HST morphology, we conclude that the gas in the superbubbles is photoionized by the obscured active nucleus. We suggest that this type of structure might be related to the spatially extended H i absorbers that are detected in front of many high-z radio galaxies. We also suggest that we may be witnessing the destruction of the extended emission-line region. In addition, we investigate the nature of the emission-line brightness asymmetry in MRC 0406−244: we conclude that this asymmetry is due to an asymmetry in the mass of ionized gas, confirming the scenario of McCarthy, van Breugel & Kapahi, and leading us to reject that of Gopal-Krishna & Wiita.