I had a similar idea a few days ago, but mine worked through an experimental Ancient knossos varient that the GTVA uncovered. It would lead into a universe where the Vasudans had won the TV war, the GTI had never encountered and provoked the Shivans, and the Great war never happened. The Vasudans were now running the galaxy, trying to fend off Terran rebels, completely unaware of the Shivans existence. Their weapons were a sort of cross between FS1 and 2, no beams, but a sort of VSL (Vasudan Super Laser) and some very powerful, huge missiles (like ICBM size). The arrival of a fully operational, fully beamed hecate messed things up a little, though. The crux was of the campaign was to be thus - The dimensional knossos dropped them off in some out of the way system, and they begin exploring, eventually running into hostile vasudans, who they absolutely destroy with beams and advanced fighters (Ares, Erinyes etc.) They then meet some terran rebels, who assume they are some sort of new rebel faction, and they ally with each other, the rebels intending to use beams to overthrow the Vasudans, the GTVA crew hoping to find a way back home. The player then goes through a series of missions, both for the rebels and the captain of his ship. Eventually, they return home through the Gamma Drac Knossos, but this alerts the Shivans to their prescence, and they begin pouring into the GTVAs dimension. Eventually, GTVA command decides to destroy the interdimensional knossos and the campaign ends.
BTW, if anyone else wants to do this, go ahead. I'm not intending to use the idea any time soon.
