A reconfigurable, protocol indifferent bit stream-processing engine, and related systems and data communication methodologies, are adapted to achieve the goal of providing inter-fabric interoperability among high-speed networks operating a speeds of at least 10 gigabits per second. The bit-stream processing engine operates as an omni-protocol, multi-stage processor that can be configured with appropriate switches and related network elements to create a seamless network fabric that permits interoperability not only among existing communication protocols, but also with the ability to accommodate future communication protocols. The method and systems of the present invention are applicable to networks that include storage networks, communication networks and processor networks.