The Harbinger's capacity to penetrate the Lucifer's shields sure has certain consequences in terms of plot, and we eyewitness the complete destruction of Reactor 4 in the last mission. Considering how unique this scenario is, I wonder if Deneb III was initially meant as a prequel to another FS1 Era campaign during which the Lucifer could be destroyed ahead of its final run for Sol. Right now, I can't think of any other fan-made project which took this storytelling path.
No, Deneb III was intended as its own thing - a campaign vignette to fill in some missing parts of the ST:R and FS2 stories, in the same sense as Shrouding the Light: Origins. I had the story outline in mind as far back as 2007; take note of the conversation in the final ST:R mission between the Soyakaze and the Guardian.
I found inspiration for the mission 3 scenario from the following points:
1) Word of
said that the Orion in the FS2 intro was not the Galatea. Since this Orion wasn't mentioned in the FS1 command briefings, this implied it was a secret mission, perhaps a GTI mission.
2) If GTI was involved, it was a nice solution to the problem of what to use as the GTI logo.
3) Now, why would the GTI be involved in such a mission, and why commit so many resources to it? Perhaps they figured out a way to attack the Lucifer.
4) Word of
also said that the Lucifer's shields didn't make actually it invulnerable, and that more powerful weapons would be able to punch through the shields.
5) Perhaps the Harbinger was on the ragged edge of being sufficiently powerful. This would explain why a bomb used for planetary attacks (from the FS Ref Bible) would be adapted for tactical bombers.
6) At this point the mission scenario began to write itself. Per the FS Ref Bible, the Vasudans used missile prototypes to attack the Lucifer. It would make sense that the Terrans would try as well.
7) The nuking of the Orion could be explained as the Lucifer reacting to neutralize an enemy ship as soon as the ship was proven to be a legitimate threat. The legitimacy could be achieved by the successful destruction of a single reactor.
The rest of the campaign could be filled in naturally by working backwards from mission 3. For example, the identification of the planet as Deneb III was a nice extra detail from the debriefing of Enter the Dragon in FS1.