We consider cortex-like complex systems in the form of strongly connected, directed networks-of-networks. In such a network, there are spiking dynamics at each of the nodes (modelling neurones), together with non-trivial time-lags associated with each of the directed edges (modelling synapses). The connections of the outer network are sparse, while the many inner networks, called modules, are dense. These systems may process various incoming stimulations by producing whole-system dynamical responses. We specifically discuss a generic class of systems with up to 10 billion nodes simulating the human cerebral cortex. It has recently been argued that such a system’s responses to a wide range of stimulations may be classified into a number of latent, internal dynamical modes. The modes might be interpreted as focussing and biasing the system’s short-term dynamical system responses to any further stimuli. In this work, we illustrate how latent modes may be shown to be both present and significant within very large-scale simulations for a wide and appropriate class of complex systems. We argue that they may explain the inner experience of the human brain.