So here's a thought experiment: what if Modern Synthesis was in order? Like each song follows the next chronologically in the Digital Haunt Story? If that's the case, I have a theory. I think it's a story of defection in a war.
I'm not exactly sure what event Override [C] describes, as it refers more to The Subject rather than The Speaker, who this theory more concerns itself. Regardless, the important thing is that the Override is an important event, that will have large ramifications, the impetus for the War
Similarly, The Contract is about The Subject, and so I'm not sure what I can say about it. Since we're assuming Modern Synthesis is in order, The Speaker must be forming a contract with the subject after they went through the Override. I'm still pretty sure the Contract puts the Subject under the Speaker's control, in exchange for the Subject "to come alive again". In my Submission-Revival Theory, I thought this is talking about the Override, but since this is MSiO, it must be something different
Finally getting to the heart of this theory, I think Watchmaker is the construction of (the?) war machine(s), set in motion by the events of the Override and/or the Contract (or, the Override/Contract could be another step in the buildup to the war). I see this in the lyrics "Forge your aggression in the Clay" and "I'm only building what I meant/to do so many lives ago", not to mention the title: Watchmaker, someone who constructs. This is slightly less analytical, but when I listen to the outro on this song, I can imagine some grand "pan out" to reveal the machine(s).
Obviously, Versus is about the War. The beginning of the war to be more precise, in its most violent and excitement. "This is the volta", i.e., the turn, the change and "Scuttle the ships", basically, to deploy troops and naval units (to be literal). I don't feel like I need to point out every link in Versus to War, just know that the Speaker sees the War as horrible and glorious.
I think Processor takes sometime later, as the Speaker is still in the war ("Structures collapsing around me"). "Call me alumni" could basically mean they're a veteran now. They hate the war ("I want no role in your altercation" "Your war desecrates Magnum Opus"). They might also feel guilty over things they've done in the war ("My deformity", "I want to be better on the inside"). In their rage and hatred, they turn towards a way to stop the war, possibly through force ("far from the pacifist you believe I exemplify/I am the fury, I am hypocrisy" "The day I take control/the day you believe me").
In Red Queen, they begin to get allies in their quest for peace ("Allies cause you both disrupt the herd" "We can only wait and watch for so long" "all those who have been/Sidelined, a lifetime's conviction unstable" "Unify behind false enemies" "Misery loves company" "You gravitate to my defection"). "Red Queen" could refer to their leader as well ("Toast to the Red Queen").
As for Angel Lust, they begin to make their move. They know that their protests will not be seen favorably "And though we'll face the spite, of thousands/And cynics they will try, to tempt and change our minds/We'll keep our faith alive, we'll raise our voices". This definitely has more of a religious theme. If the Speaker is talking about the rebels they gathered, they may have organized under a religion ("We know we'll never die alone and frightened/Just closer to the last communion without her").
In The Life of a Ghost, the Speaker has possibly lost a battle (would make sense if we treat MS as a story, as TLoaG would be at the end of the second act), or possibly just tired and worn out from the fighting in the war and against the war ("But I'm tired and I'm worn through" "Journey downward from a height"). They might also be questioning their journey and wondering how they got there ("Lost in thoughts of where I am").
In After the Flags, the Speaker has gained resolve ("'But still it moves' I heard you cry" could refer to the status of their movement; it is still alive). They once again criticizes the participants in the war ("'Come on son, do your country proud!'" "And wash our hands of campaigns for the self-assured now" "I wanna die for a reason/I wanna kill for a cause"). One part I find interesting is "Eyes are wide; we have been misled", which could refer to a betrayal, possibly by their leader, which would cause the fall between Angel Lust and The Life of a Ghost. Or it again, could be referring to the leaders of either side of the war.
Nebula is likely spoken right after After the Flags. The Speaker prepares for some final battle, reflecting on their experiences. "This is my suffering" could be how they committed crimes in the war, but now, after they "see through your crystalline fantasy", they can "Speak free with the faction". "But now, there's no one beside me/They've fallen behind" is the loss proceeding The Life of a Ghost. The section "Hey there you lost boy, just look at what they've done to you/They've poisoned the well of your mind but you'll make it through" could be a brief mention of some soldier blinded by nationalism/religion and hatred for the enemy.
This would be the conclusion, after all battles have been fought. "Wait inside/By the fire and we'll talk a while" would be the Speaker calling the Subject to rest with them and reflect on experiences. "I'm sorry that I let you down, let you down, a lifetime ago" would be their continuing regret of events before they defected, which was frowned upon by the Subject. "Will I feel absolved/At the moment when we have it solved?/A panacea for the absent soul" is, again, their feelings of guilt over their actions. "I wanna say/to all I leave behind/And to those I'll never find/That I need you to understand, understand, you're not on your own, you're not on your own" could be a message of hope and apology to their fallen comrades and future like-minded individuals.
Finally "As lines fade out, you will illuminate/And lead a way back home" is an echo of the words from Processor. In Processor, it was the Speaker leading the Subject (as part of the contract?), but now the Speaker requests to be led, tired and feeling done with fighting.