Fanfic Doesn't matter if it's not finished, there is no redeeming this fic.
Alright, let me start right off the bat by saying that, even though it's not yet finished, this entire fic's premise is to take likable characters and make them villains. If you're going to do that, then you've failed as a fanfic writer before you've even begun.
In the series proper, Twilight Sparkle has always taken time to put a lot of thought into responding to new and unfamiliar situations, but in this story, she takes a cursory glance at the human race and then writes them off as the bad guys, going so far as to provoke all-out war.
While it would make sense that she wouldn't necessarily make the best judgment in such a situation, the fact that Princess Celestia actually stands by this statement is utterly baffling.
Did the author somehow miss that learning to understand, and more importantly accept others' differences is the central theme of the actual show?
Twilight has always been portrayed as a character who would at least try to be open-minded in an unfamiliar circumstance, and while she may not necessarily succeed, having her make a broad generalization for an entire species is not something that she would do.
And then Princess Celestia, who's been shown in canon to put as much effort as possible into establishing some sort of mutual understanding, goes against everything she's ever been shown to stand for by continuing this position. I don't believe it for one second.
The story itself also draws uncomfortable parallels to World War II, and it appears that the Equestrians for Humans organization is based off of the White Rose, a resistance group against Nazi Germany.
So, the Equestrians are basically Nazis now. It doesn't matter where the fic goes from here or if they learn their lesson, this is a premise that utterly fails to begin with.
As per Godwins Law, the discussion ends here.
Fanfic Behold the deconstructor fleet! (Armed with 16In guns)
The problem that faces most people reding this fic is that the don't know what it is.
It's not an Original Flavor fic based on canon MLP:Fi M.
It's not a Humanity: Fuck Yeah! fic.
It's not a Revenge Fic of the Conversion Bureau ponies getting nuked.
It's not an anvil-heavy "moral" lesson about humanity.
What it really is, is a deconstruction of the entire Conversion Bureau genre. Whereas the original failed to adress the ethical issues regarding ponification and made a massive Karma Houdini out of Celestia, this one makes those issues paramount to the story, putting them in the spotlight and hadling them realistically. Where the original had Wish Fulfillment, Humans Are The Real Monsters, and Can't Argue With Ponies, this one has intrigue, political fallout and sympathetic characters. On both sides.
Here, Celestia's misanthropism is put in display right from the very beggining, and rather than submit to it as in the original, humanity reacts as it would have done so if the situation hade presented. We disagree, we fight back, as any other human would've done so.
However, what is truly remarkable is that the author makes sure to not make any side an utter monster, or a complete saint. There are humans that react violently to the ponies, with racism and bigotry to match that of the ponies themselves. At the same time, there are also ponies who don't agree with the ponification, and humans who believe that a species can't possibly ber represented by their worst elements.
All in all, an interesting, compelling fic that makes its world look real.
Fanfic Too soon to say
After re-evaluating this fic, I have changed my opinion on it and edited the review. It has some editing problems but I clearly jumped the gun on a couple points. Although the followers of the story in the comments section tend to be MORE THAN A LITTLE rabid, the author has more appreciation for subtlety than I originally realized - something rather difficult to convey in the Anvilicious TCB genre.
I still feel like the story in general is unfairly biased toward the pro-human viewpoint, mostly by lack of dissenting voices in the narrative. Additionally, Equestria's motives are a little unclear. Although the author seems to take the view that the ponies are essentially alien invaders bent on genocide, it isn't that clear-cut in most Conversion Bureau stories. The ponies are often legitimately trying to help humans in their own way and don't understand why humans would be upset, or they have no more control over the merging of the worlds than the humans do, or any number of other explanations. It's the author's story and he can give them whatever motives he wants, but I find it a little jarring - especially since the topic is never really discussed.
Although I'm still not an enormous fan, it's a little early in the storyline to be making judgements just yet. We'll have to wait and see where things are going.
Fanfic A long and enduring legacy
Not Alone, hands and hooves down, is the most influential story in the Anti-TCB War Fic subgenre. It's not the first of its kind, but it codified many of its most quintessential tropes, much like how Chatoyance herself codified much of the lore of the more traditional TCB stories. And it earns that title for good reason.
Not Alone runs on injecting nuance to the genre in a thoughtful and measured way. Grey morality is the dominating factor, making use of a diverse ensemble of characters who are all likable and sympathetic. Neither side is portrayed as being inherently better or worse than the other. Even the villains are treated evenly, being well-meaning but going about it in the worst ways. The consequences that follow are logical and well thought out. It’s got a subtlety to it that is refreshing considering TCB authors on both sides usually have a penchant for the bombastic (I myself am guilty as charged).
I know Starman Ghost has zero desire to revisit this story and probably looks back on it with disgust and shame, but it is still a good story on a technical level, and considering the source material (the show itself and the original fanfic this was based on), that’s saying something. While it's a bit more... bare-bones compared to more thorough deconstructionist efforts like The Spectrumverse and The Negotiationsverse, its legacy is firmly cemented as the fanfic that inspired the core of them both. This story’s greatest accomplishment was that it gave the Anti-TCB side a story that allowed us to fight back against the tide of misanthropic "I wish I could be a pony" cringe-fests dominating the early days of the TCB genre in a nuanced and intelligent manner without going square into "humanity fuck yeah" territory. And that makes me happy. Thank you for everything, Not Alone.