Part III — The Gate Protocol
Part III presents the full restoration architecture developed in response to the collapsed, pathobiont-dominant system detailed in Parts I and II. The Gates translate ecological succession, mechanistic constraints, and systemic load dynamics into a sequenced, non-interfering intervention structure.
Each Gate exists because of a defined structural requirement:
biofilm architecture had to be disrupted before suppression; suppression had to be followed by binding; nutrient and mitochondrial support required stabilization; enterohepatic interruption depended on epithelial resilience; ecological restoration required all prior pressures to be reduced.
This section documents the functional purpose, mechanistic roles, timing logic, dependencies, and completion indicators for Gates 0–6. It clarifies how each Gate aligns with fasting-state and fed-state physiology, how interference is avoided, and how sequencing maintains ecological feasibility.
→ Part III is the operational structure that converts mechanistic insight into an actionable, temporally coherent restoration pathway.