Hyper-luminous infrared galaxies (HyLIRGs) lie at the extreme luminosity end of the IR galaxy population with $L_{rm IR}>10^{13}$L$_odot$. They are thought to be closer counterparts of the more distant sub-mm galaxies, and should therefore be optimal targets to study the most massive systems in formation. We present deep $Chandra$ observations of IRAS~F15307+3252 (100ks), a classical HyLIRG located at $z=$0.93 and hosting a radio-loud AGN ($L_{rm 1.4 GHz}sim3.5times10^{25}$ W/Hz). The $Chandra$ images reveal the presence of extended ($r=160$ kpc), asymmetric X-ray emission in the soft 0.3-2.0 keV band that has no radio counterpart. We therefore argue that the emission is of thermal origin originating from a hot intragroup or intracluster medium virializing in the potential. We find that the temperature ($sim2$ keV) and bolometric X-ray luminosity ($sim3times10^{43}$ erg s$^{-1}$) of the gas follow the expected $L_{rm X-ray}-T$ correlation for groups and clusters, and that the gas has a remarkably short cooling time of $1.2$ Gyrs. In addition, VLA radio observations reveal that the galaxy hosts an unresolved compact steep-spectrum (CSS) source, most likely indicating the presence of a young radio source similar to 3C186. We also confirm that the nucleus is dominated by a redshifted 6.4 keV Fe K$alpha$ line, strongly suggesting that the AGN is Compton-thick. Finally, Hubble images reveal an over-density of galaxies and sub-structure in the galaxy that correlates with soft X-ray emission. This could be a snapshot view of on-going groupings expected in a growing cluster environment. IRAS~F15307+3252 might therefore be a rare example of a group in the process of transforming into a cluster.
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