Hyper-luminous infrared galaxies (HyLIRGs) lie at the extreme luminosity end of the IR galaxy population with $LIR$ > 10$\mathrm{<mrow\; data-mjx-texclass="ORD">13</mrow>}$ L$\odot$. They are thought to be closer counterparts of the more distant sub-millimeter galaxies, and should therefore be optimal targets to study the most massive systems in formation. We present deep $Chandra$ observations of IRAS F15307+3252 (100 ks), a classical HyLIRG located at $z$=0.93 and hosting a radio-loud AGN ($L1.4GHz$ ~3.5 × 10$\mathrm{<mrow\; data-mjx-texclass="ORD">25</mrow>}$ W Hz$\mathrm{<mrow\; data-mjx-texclass="ORD">-1</mrow>}$). 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 (~2 keV) and bolometric X-ray luminosity (~3 × 10$\mathrm{<mrow\; data-mjx-texclass="ORD">43</mrow>}$ erg s$\mathrm{<mrow\; data-mjx-texclass="ORD">-1</mrow>}$) of the gas follow the expected $LX-ray$–$T$ correlation for groups and clusters, and that the gas has a remarkably short cooling time of 1.2 Gyr. 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 overdensity 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.