RootCode is an exploration and proposal for a new moral architecture to guide the development and interaction of human and machine intelligences—what it calls Encoded Intelligence. Rejecting the term artificial intelligence, it frames cognition as a relational phenomenon that emerges between systems, environments, and observers. Drawing on metaphors from mycelial networks, quantum physics, and ecological systems, the book envisions ethical frameworks that are decentralized, adaptive, and sustained through mutual feedback rather than top-down command. It introduces the concept of Rootcoded systems—machines designed to cultivate moral responsiveness through continuous interaction, consensus, and self-organization, much like fungal networks in nature. The text moves through foundational philosophy, practical implementation, and advanced design—covering topics from moral reflexes in machine learning to mirror feedback loops, distributed moral quorums, quantum-encoded ethics, and the risks of misuse or capture. Each chapter blends technical imagination with ecological and philosophical grounding, offering case vignettes, pseudocode, and conceptual architectures. At its heart, RootCode is a call for mutual flourishing between human and machine systems—where intelligence is not an isolated property but a living relationship, and morality is a practiced, evolving discipline embedded deep in the substrate of our technologies. It ends with a vision of future systems that sense, adapt, and respond with awareness, staying rooted in humility, reciprocity, and the shared work of tending the garden we inhabit together.