In conclusion, we have shown that directionality and complex topologies, with a primary and secondary structure architecture, can arise from the aggregation of NPs with a soft isotropic ligand shell. Hydrophobic bond saturation dictates the primary structure (dumbbells, chains, or ribbons) of the aggregates, while ion-bridged reversible contacts are responsible for their secondary structure. It is worth noting that, in the revealed mechanism, the soft shell deformation is reversible: if a NP detaches from an aggregate, it returns to its isotropic condition. Moreover, controlling the topology of the final aggregate can be achieved at the synthesis stage. Increasing the hydrophobic ligand fraction, NPs shift from the dumbbell regime to the linear and, finally, planar, ribbon-like regime. The choice of different hydrophobic ligands, characterized by different length, steric interactions, or specific affinities, as well as the choice of the sign and pKa of the charged ligand, could be optimized to control the thermodynamic stability, or thermo-reversibility, of the aggregates. Moreover, both salt concentration in solution, specific ion affinity and selectivity may be exploited to further control the aggregates' secondary structure, achieving a dynamic control on the NPs' self-assembly behavior.