The present crisis of foundations in Fundamental Science is manifested as a comprehensive conceptual crisis, crisis of understanding, crisis of interpretation and representation, crisis of methodology, loss of certainty. Fundamental Science "rested" on the understanding of matter, space, nature of the "laws of nature", fundamental constants, number, time, information, consciousness. The question "What is fundametal?" pushes the mind to other questions → Is Fundamental Science fundamental? → What is the most fundamental in the Universum?.. Physics, do not be afraid of Metaphysics! Levels of fundamentality. The problem №1 of Fundamental Science is the ontological justification (basification) of mathematics. To understand is to "grasp" Structure ("La Structure mère"). Key ontological ideas for emerging from the crisis of understanding: total unification of matter across all levels of the Universum, one ontological superaxiom, one ontological superprinciple. The ontological construction method of the knowledge basis (framework, carcass, foundation). The triune (absolute, ontological) space of eternal generation of new structures and meanings. Super concept of the scientific world picture of the Information era - Ontological (structural, cosmic) memory as "soul of matter", measure of the Universum being as the holistic generating process. The result of the ontological construction of the knowledge basis: primordial (absolute) generating structure is the most fundamental in the Universum.