The Administrative Department (AD) serves as the executive authority and strategic governance body of Site-89, overseeing high-level policy, ethical governance, and interdepartmental oversight to ensure all operations align with Foundation directives.

Internal Affairs manages the day-to-day functions that keep Site-89 running: personnel management, facility operations, budget administration, documentation, and interdepartmental coordination. The operational backbone of the Foundation.

The Scientific Department (ScD) has multiple divisions specializing in research, anomaly testing, occult studies, and medical oversight. All divisions work to understand anomalies and ensure containment procedures protect the public.

The Security Department (SD) ensures site security, anomaly containment, and personnel protection. All requests are processed through Security Command to the appropriate subdepartment.