The ability to understand, predict, secure and exploit the vast array of heterogeneous network of things is phenomenal. With the ever-increasing threats to cyber physical systems and Internet of Things, security on those networks of data-gathering sensors and systems has become a unique challenge to industries as well as to military in the battlefield. To address those problems, we propose a trusted computing protocol that employs discrete Trusted Platform Modules and Hardware Security Modules for key management, a blockchain-based package verification algorithm for over-the-air security, and a secure authentication mechanism for data communication. The IoT-based Trusted Computing Protocol implements integrated hardware security, strong cryptographic hash functions, and peer-based blockchain trust management. We have tested the protocol under various circumstances where devices have built-in securities while others do not. We apply the new protocol to a SCADA system that contains more than 3,000 edge devices. The preliminary results show that proposed protocol establishes trust, improves security, integrity, and privacy.