The bonding and organization of 1,1,2,3,4,5-hexaphenysilole (HPS) molecules adsorbed on Cu(111) and Ag(111) surfaces has been investigated using low-temperature scanning tunneling microscopy and X-ray photoelectron spectroscopy. In room-temperature-prepared samples, HPS molecules form extended networks that exhibit hierarchical organization stabilized by pi-pi interaction between exocyclic phenyl groups. After 430 K annealing on Cu(111), the compound is chemically altered as evidenced by Si 2p core level shift. This change is accompanied by a different adsorption configuration and a transformation of the assembled structures from networks to uniformly sized chiral clusters. The clusters, each composed of three molecules, are dispersively distributed on the surface. Monte Carlo simulations signal that this new phase can be understood as a result of competing long-range repulsions and short-range attractions. After even higher annealing at 520 K, the clusters dissolve and the exocyclic phenyl moieties undergo a cyclodehydrogenation reaction to form a polycyclic aromatic compound incorporating a silole moiety. In sharp contrast, on Ag(111), the HPS molecules do not show these changes but desorb from the surface at elevated temperatures. Our results demonstrate that the two-dimensional supramolecular assembly of intact HPS is insensitive to the choice of substrate at room temperature, but at high temperatures, the substrates chemical activity can induce selective chemical transformations resulting in a significantly different assembly behavior.