The prologue sounds like something i'd think up. My missions tend to revelove around a big ship being destroyed by a bigger ship, which is blow up by something even bigger.
Second Colossus=Unlikely
Built in Secret=Hahahaha
Inter-system jumps, not node-dependant=Way to kill the game.
Better idea:
While the fleet is headed for Capella an unknown signal is detected near an instable node in Capella. A destroyer is sent to investigate, it losses contact with command and disappears. No debris is detected by an AWACS sent to scan the Saths and investigate the disappearance, but there's a wierd subspace energy in the area. Capella explodes.
More mystery and doesn't completely screw with the basic elements of the game. *cough*nodes*cough*.