Premise: Don't mess with the Shivans
(The premise is the point the story makes. It is the ultimate conclusion that the listener/reader of the story must draw.)
Admiral Bosch wanted to make a new, prosperous alliance with the Shivans, using his ETAK device. We know that some kind of communication did take place, and that some Shivans made contact with the crew of the NTF Iceni, killing everyone on board save Bosch, who they took. We don't know what happened to Bosch or to what extent they communicated with each other, but it cost him his rebellion - which he brought about for his own goals with the Shivans - and he couldn't be sure as to what the Shivans would do with him.
The GTVA thought they were achieving major victories when they destroyed the Ravana and the first Sathanas, only to discover 80 similarly powerful Shivan juggernauts on the way. The lost the Colossus, which they built specifically to combat the Shivans, and it couldn't even put up a fight on its second encounter with the Sathanas. To make things even worse, the Destroyers used a weapon of massive scale to cause the Capella star to go supernova.
Alternately, if you believe that the Shivans are merely defending their own territory, the story's premise could be: "Curiosity kills the cat." The deeper the GTVA pushes into the nebula, the bigger problems arise. When the Psamtik discovered the second Knossos, which was apparently leading into Shivan space, the Shivans decided to utilize their entire fleet to fend off the trespassers. Any race that knows about the means to get into Shivan space is a threat that must be removed.
Narrator: Alpha 1 (main) Bosch (auxiliary)
While Alpha 1 doesn't say a word, it is through his eyes that we see events unfold. We know only what he sees and what he hears.
While Bosch speaks in some missions, he does so in the context of conversing with GTVA officials. In this role, he is a consciously unreliable narrator who won't reveal his motives for doing what he is doing, adding an atmosphere of mystery to the story. Of greater interest are his monologues. Through his lonely contemplations that the player "overhears," we learn that things aren't what they appear.
Major Theme: Growing arrogance
The destruction of the SD Lucifer and the construction of the GTVA Colossus made the GTVA grow arrogant in their technological superiority. The Shivans, the biggest threat the GTA and the PVN faced over the course of their respective histories, were totally defeated. There are several lines over the course of the campaign that make this point. One of the corvettes in The Great Hunt (FS2) utters: "We'll show them what firepower is all about," a pilot in the same mission calls the victory over the Great War "a miracle," implying that the GTA-PVN alliance did something totally unexpected. After its dreaded and shocking introduction, the Ravana was destroyed in the subsequent mission. Notice that the Ravana and the Lucifer are similar in terms of design: with two heavy beam cannons facing forward. Of course, Command relates the victory over the Ravana to the victory over the Lucifer. At this point, the GTVA could very well believe that they caught up with the Shivans.
The command briefing in Return to Babel declares a complete victory over the Shivans. It is clear from Admiral Khafre's phrasing that they believed the Sathanas was the best the Shivans had, which they could destroy by the very ship specifically built to combat Shivans.
Recurring Symbol: The nebula
Limited field of sight inside the nebula is not only a physiological limitation that helps gameplay and to build up tension, but it's also metaphorical. Limited field of sight means a limited field of understanding of events through the "Understanding is seeing" conceptual metaphor. Consider the English phrase: "I see your point", which means "I understand." The GTVA didn't see what they were going after until it came to them (the two Sathanas juggernauts, and to a certain degree, the ETAK's true purpose).
Rising Action: Entering the nebula; the hunt for Sathanas 01; pursuing the Iceni
Falling Action: The Azrael gets away with Bosch and the appearance of a second Sathanas
Foreshadowing Kappa 3's reemergence and his line: "Get the fleet out of the nebula. There's something out there, Command!"
Climax: Bosch using ETAK; the discovery of the juggernaut fleet
