Instrumented networks and platforms having target subjects (devices, transactions, services, users, organizations) are disclosed. A security orchestration service generates runtime operational integrity profiles representing and identifying a level of threat or contextual trustworthiness, at near real time, of subjects and applications on the instrumented target platform. Methods and systems are disclosed for network flow and device / platform remediation in response to reconnaissance-based intelligence correlation based on network monitoring, to accomplish network flow remediation and device / platform remediation. In an embodiment, a system receives system warnings and endpoint threat intelligence. The system correlates risk based on inputs from sensory inputs that monitor network activity, system configuration, resource utilization, and device integrity. The system then performs a calculus of risk on a global security context including endpoint assessment reports and sends system warnings based upon the endpoint threat intelligence. The system includes a remediation engine for receiving real time directives to control the device.