Well its been more than a year and I've come back to the pile of notes on the back of desk (I need the space because I'm soon to GM a X-Wing: The Miniatures Game-campaign) and rather than forcing to write an end to this I'm going to spill the beans in a plain fashion:
So what you read in Part 1 is the end of Faces of Treason when you have GTVA forces fighting each other over the fact well *something* is wrong in the systems beyond Regulus. At the time I penned FoT it seemed like a clever twist to make those events not matter anymore because bigger things were in motion. In Part 2 we get to the main villian of the WotW-storyline who gets is head-start on everyone else.
Epicenter would go with the GTSC Haeckel to continue to dirft in space with the first wave of Constructor ships beginning to rip the ship apart for usuable parts. Days into the mess near the end of the ship a rescue party arrives that comes from an unexpected direction. The event that caused the Haeckel to be crippled in the first place was the discharge from a subspace-drive that is not limited to node-to-node flight for intersystem transit; a technology the GTVA has not mastered because of the large quanteties of energy required to activate it, and the Shivans don't use because it's deployment is followed by a huge discharge of radiation as the ship returns to normal space (practically wrecking everything in the nearby area). Most of what was coming would be technobable about this new type of subspace engine I made up for the sake of the story.
This would tie in into the larger Workings of the Warp-storyline as the Constructor-"invasion" and the reactions from both the Shivans and the GTVA would be kicking of the story. The Shivans would swoop in to stop the Constructors (explainations of that changed over the years I've been on this; and non of it really sticked). The GTVA would see the Constructors as a new threat to its existence or as technological treasure to be exploited for their fight against the Shivans (depending who would be calling the shots at any given point in the GTVA command structure).
And here comes one of the big twists of the story:
The people who are coming to rescue the survivors aboard the Haeckel are members of the NTF (two of who are familiar faces (http://www.freespacemods.net/download.php?view.883)) who are with the initial Shivan response force which is trying to get ahead of things. The NTF members have come make sure the GTVA steps aside and let's the Shivans and the Constructors duel this out amongst themselves. Bringing the Haeckel survivors back at that time seems a good idea but when the NTF guys get wind that the mission of their third partner (guess who) went sour, they abandon their plans to reason with the GTVA and send the Haeckel survivors on their way alone (though not without ensuring they are rescued by GTVA forces).