I designed the conceptual workflow and led the numerous group of people that worked to first define and then simulate the CTA instrument response to all its main astrophysical problems, from an initial undirected brainstorming to key science program definition. I worked on identifying gamma-ray binaries and pevatrons, physics exploitation of the Galactic surveys, evaluating its confusion, simulating cosmic-ray propagation and interaction, studying CTA response to pulsar wind nebulae, supernova remnants, and pulsars, studying the influence of the site selection in regards to astrophysical observations, and others. An initial account of the group's work was summarized first in an Experimental Astronomy article, then in an Astroparticle Physics special issue I co-edited in 2013. Relevant internal documentation from this period includes the initial report on the scientific requirements (D. F. Torres, et al., SCI-LINK/121120, 2012), as well as the design concepts (arXiv:1008.3703), and successive technical reports, some submitted as deliverables of an EU Infrastructure project, for which I was responsible of the science chapters. Finally, all this work ended in the CTA Key Science Programs, accounted in the book ‘Science with CTA’ (World Scientific 2019, arXiv:1709.07997) which I co-edited too.