A thesis concerning the ontology underlying the formation of structural-dialectical systems based on the implications of the phenomenon of Emergence is presented. Emergence refers to the unexpected appearance of discontinuities which segment on-going traditions. The Western philosophical tradition is used as an example focusing on motifs introduced in the Phaedo, the transition from Hume to Kant, and contemporary ontology. Emergence (as structurally coded artificial novelty) is posited to be the opposite of the phenomenon of Nihilism (erratic change projected by the structural system rendering the formal system visible), and both are functions of the ideational process. The ontological basis of Emergence is sought by exploring the articulation of the form of the ideational process, through which structural theoretical systems are produced, called the 'ideational template'. It has three parts: 1) SHELL—The expanding wave of logical connections by means of triadic formalisms seen on the Nihilistic background; 2) CORE-—The unfolding structural dialectical underpinning to the formal system in which artificial emergences appear; 3) CENTRE OF THE CORE—Fragmentation of the concept of 'Being' which provides the ontological foundation for the Formal/Structural system. The ideational template is destructured in order to show the feasibility of an alternative metaphysical model based on disconnecting opposite qualities instead of focusing on form and structure as the ideational process does. This brings attention to the principle of 'No Secondary Causation' as a means of tracing back artificial emergence within structural systems to a genuine emergence of all entities and qualitative opposites to a single source (called by Plato 'the Good') indicated by the methodology of logical disconnection rather than syllogistic connection. The alternative to logical ideational connection is called the 'logic of disconnection'. The metaphysical basis of a qualitative science as distinct from quantitative Western science is posited.