I want to know if something like this has been done before.
The idea is that the GTVA creates a new superdestroyer controlled by an AI system designed to need a minimal crew and be faster and more efficient than a ship controlled by Terran or Vasudan pilots. It also has squadrons of remotely-controlled fighters that can coordinate and work together with amazing effectiveness.
However, during a combat test, the AI goes rogue and kills all of the crew aboard it by venting its atmosphere into space, and then destroys many other GTVA ships before jumping out to an unknown destination.
The campaign focuses on hunting it down, defending ships, stations, and planets from its raids, and finding out why it malfunctioned. (The answer is that they used Shivan computer technology when designing it, and couldn't properly predict its actions). The final battle involves the AI superdestroyer, having stolen the blueprints for Knossos technology, attempting to build and stabilize a node into Shivan space, to cause a new Shivan invasion, and you have to stop it.