Actually, I've already got a sort of outline fleshed out in my head, and Dundradal got it sorta. (Again, props to Shipgate for the O'Brien reference!)
The story would be a detective-type thing, starring a normal homicide detective and a military intelligence officer.
The whole thing would start with a murder of someone working in the Foreign Ministry whom MI suspected was involved in espionage activities somehow. This would occur just before the truce, say a few days, maybe a week. The homicide detective (whom I envision as female) would catch the case, and would meet the MI officer (whom I envision to be male) heading the investigation into the dead guy's suspicious activities.
Most of the story occurs during the truce.
They slowly start to unravel a whole spy ring (with requisite action scenes, drama, etc.). I envision a scene of great drama in which they have a suspect in custody, who somehow tips them off to the bombing, and the two racing to the site to try and stop it, only to arrive minutes late.
Unfortunately they can't work with Vance Richards, cause he's off with Jason and Kruger having fun of his own.
Somehow they gather evidence concerning the Foreign Minister and begin to suspect her (this happens before the bombing). They take it to the MI higher ups, who take them to brief the President in private. He's obviously hostile to the whole thing, orders them to stay away from the Foreign Ministry. Of course, our daring duo will have none of this, and they continue to investigate and gather evidence, all the while conflicting with their superiors who have ordered them off the case. There could also be some fun instances where the confron the Foreign Minister directly (anyone know her name?), but lacking evidence, they can't do anything. Of course, she alerts her Kilrathi handlers, who then try to have the duo killed. Much potential for action and drama here.
Finally, they get enough evidence and take their case to Duke (just after the bombing). He believes them, again goes to the President. There's the scene in Fleet Action where he shows the President the holos of the secret fleet, and later on the President says that he had been told about her possibly being compromised months ago. That was the results of our heros' investigation.
I'm not sure what the climax would be. Just arresting her after she refuses to resign seems a bit anticlimactic. I want more action. Perhaps she could attempt to escape the planet, but she doesn't seem like the type to try and fight her way off. Looking at Fleet Action now, after that last meeting, Jamison storms off, Tolwyn, Grecko, and the President talk some more, then the President leaves, I think he said "to take care of Jamison". Perhaps outside the meeting room he meets our two heros, apologizes or something, tells them to go arrest Jamison. But that still leaves us with no action at the end.
Hmm, I'll have to think on this one a bit more. Thoughts? Comments? Suggestions?
Or Freedom Flight's latter half? How about half of Action Stations?