We have used low-temperature ultrahigh vacuum scanning tunneling microscopy to gain atomic-scale insights into the hydrodesulfurization process. Investigations of Ni adsorbed on the basal plane of MoS2 revealed that the Ni adatoms are highly mobile due to their weak interaction with the exposed sulfur atoms. The Ni adatoms rapidly diffuse about the surface down to 77 K, and even at 4 K are easily manipulated with the STM probe tip. Spectroscopic imaging of Ni clusters adsorbed on the MoS2 basal plane reveals that their electronic structure is well suited to bind nucleophilic reactant species. From low-temperature STM images of thiophene adsorbed on Ni{110}, a bonding geometry is proposed. New roles for metal promoter atoms in hydrodesulfurization catalysis, based on these results, are suggested.