Overall was not too impressed with this. I am not too aware of the lore for your universe. Outside of reading that info dump of a backstory you made to serve as the series template for plot since the first episode of the main series. I believe you meant to build up to some shocking revelation which never really pays off to be honest. The use of the word Fraternization in this context is more or less a "You keep saying that word I do not think it means what you think it means." Not to mention I am fairly certain these human agents were still in the employ of your Gary-Stus oops I meant main characters. So why just willingly kill them off? Not to mention cause the death of elite troops in the process which will take a bit to fill the gap in terms of training.
Speaking of which removing the human element of the faction in favor of what amounts to be Stormtroopers with yellow blood would also have an impact on tactics. On the matter of tactics While the idea of a miniature civil war in which two groups fight each other in the same base sounds excellent on paper. The actual execution leaves much to be desired. I say that because it seems all the enemies went to the Academy of Stand Still Like A Jackass and Let Your Foe Exterminate You and Your Squad. Not to mention why would I assume to be one of the heroes of the series callously order the deaths of his own men simply for not being ATP?
Then again he did try to murder your self-insert I mean original character by throwing him into an arena after reviving him for some reason? One final complaint is the movement why does it feel that with every trigger pull, step, or swing of a melee weapon the characters might as well be swimming in a stream of mayo in a 1950's sc-fi suit powered by Comcast Broadband?
Final verdict: 1 star mainly because of the original idea which had enormous potential but the execution just fell flat when needed most.