Simulacra Naturae is a collaborative media installation exploring the entanglement of digital morphogenesis and the interplay between biological and artificial intelligences. Brain organoids drive simulations of agent-based ecosystems such as flocks, slime molds, and termites. Their spontaneous neural activity modulates the behavior of these agents, influencing real-time generative visuals, spatial sound, sculptural forms, and living plants within the installation. By merging neural data, algorithmic growth, and material fabrication, Simulacra Naturae creates a hybrid ecosystem where cognition and agency emerge through co-evolving interactions between code, matter, and living systems. This mediated environment invites reflection on synthetic ecologies, distributed intelligence, and the blurred boundaries between simulation and sensation.