Thanks to Chris, we also located the second piece of lost Secret Ops fiction. This was mistakenly posted to alt.games.wing-commander by Boomer about two months before SO was released... and he asked everyone to disregard it, since it spoiled the game. Oddly, the topics brought up in the e-mail never really appeared in the game. Here it is, for posterity:
From Confed Intel. *Security Channel Only*
All intelligence analysis lead us to believe the Aliens entered in our system to look for some specific object or technology. The military incursion was only a diversion. This is evidenced by the fact all after-action battle reports clearly indicate that loss of life or equipment (to include capital ships) meant nothing to the hive. Of greater importance to the Aliens was the mission to locate the object.
Further, post encounter analysis of their collective behavorial attributes indicate the location of the subject of their mission was indeed discovered
It is therefore expected we may be witnessing the emergence of a secondary wormhole likely constructed during (or prior) to the recent encounter to ensure the delivery of the artifact.
Summary: The most alarming aspect of the post-encounter analysis is that even though in each case we won the battle it appears they did succeed in their ultimate goal.
It is then imperative we clearly understand all of our knowledge of the Bugs is thus far based on pure speculation. Their true motivations are not explained solely by their invasion.