We often observe phenomena connected to the actions of collectivities or populations of similar unorganized elements, or the actions of individuals (agents) of some species, which seem directed by an invisible hand guiding the analogous behaviors of the individuals to produce an emerging collective (macro) phenomenon. Such phenomenon cannot be reduced to the simple sum of the effects from the individual (micro) actions; rather, it is the result of the “combination” of these individual actions that conform to the collective behavior, which in turn conditions the behavior of the individual, in a macro-micro feedback. The awareness of the existence of traits common to collective phenomena leads to the formulation of the Combinatory System Theory to explain the genesis and maintenance of these macro phenomena. This chapter formally presents the basic ideas behind the theory, analyzing in some detail the logic of combinatory systems and their constitutive characteristics.