Chemical vapor deposition has proven to be one of the most promising approaches to achieve large-scale and high-quality ultra-thin layered materials in general, and single- and few-layer transition metal dichalcogenides in particular. Therefore, the study of the conditions affecting the growth and the obtained structure (morphology and chemical composition) is of crucial importance in order to improve its consistency and generalize these methodologies for the growth of other 2D materials. Here, we show that the growth temperature and pressure have significant effect on the final MoS2 morphology, leading to completely different results: homogeneous surface coverage with inorganic fullerenes, loosely surface bound thin elongated hexagonal nanostructures and single-layer domains. This work focuses on the characterization of the less common elongated hexagonal nanostructures, including their growth mechanism, phase, chemical composition, doping and electronic properties. An interesting epitaxial relation between the MoS2 layers and the metal oxide particle, which may have practical implications in the future, is demonstrated and discussed as well. Finally, we demonstrate the in situ doping and alloying to form MoS2-xSex nanostructures. This work provides new insights into the growth mechanism puzzle of MoS2 nanostructures.