We examine the conversion of heavy-fuel oil waste generated by marine-transport operations into drop-in transportation fuels. The proposed conversion process comprises two steps: (i) hydrotreatment and (ii) fluid catalytic cracking (FCC) under industrially relevant conditions. CoMo/Al2O3 is employed as the catalyst for hydrotreating, primarily aimed at sulfur reduction. In the second stage, a highly intensive study of the FCC over an equilibrated steamed zeolite catalyst is performed. We provide a complete analytical overview of all the products and byproducts of these two reactions, including the coke deposited over the FCC catalysts using various characterization techniques, including high-resolution mass spectrometry. The hydrotreatment eliminates 67% of sulfur present in the original ship oil, while the cracking yields up to 47 wt% high-quality gasoline, containing 37 wt% aromatics, and 23 wt% i-paraffins. Based on the molecular-level characterization of the formed coke species and the performed parametric study, this work provides insights into the optimum operational conditions for minimizing coke deposition and improving the gasoline yield and quality.