The addition of dodecanethiol to a solution of oleylamine-stabilized gold nanoparticles in chloroform leads to aggregation of nanoparticles and formation of colloidal crystals. Based on results from dynamic light scattering and scanning electron microscopy we identify three different growth mechanisms: direct nanoparticle aggregation, cluster aggregation, and heterogeneous aggregation. These mechanisms produce amorphous, single-crystalline, polycrystalline, and core-shell type clusters. In the latter, gold nanoparticles encapsulate an impurity nucleus. All crystalline structures exhibit fcc or icosahedral packing and are terminated by (100) and (111) planes, which leads to truncated tetrahedral, octahedral, and icosahedral shapes. Importantly, most clusters in this system grow by aggregation of 60-80 nm structurally nonrigid clusters that form in the first 60 s of the experiment. The aggregation mechanism is discussed in terms of classical and other nucleation theories.