For anyone who is still actually reading this story after such a long wait, wow! Anyhow, major news update: I am rather excited about a canon story that I am going to write, taking the perspective of a stormtrooper in the waning days of the Empire. I have kind of lost the excitement of writing this AU, but I don't want to leave you guys hanging. So, while this story remains sadly unfinished, I would like to give you all a plot summary for what the rest of the series would be.
Book 1: Fall
This book would have had about nine more chapters. They would consist of Anakin and Padmé joining the True Jedi in the Maw. The True Jedi eventually get the idea to reprogram and reactivate the CIS droid army and use it to declare war. Many of the former CIS systems are already fed up with Mace at this point, and want liberation. After a lot of action and chaos, the True Jedi, in the end, get the army activated and serving them. Mace's clones are spread too thin, and the droids are too concentrated, so the True Jedi gain a lot of territory. Many planets, even former Republic ones, consider Mace's "triumvirate" of Jedi, Senate and Chancellor to be a form of dictatorship, and join the True Jedi army. Maul joins Mace's cause, and becomes the highest ranking New Jedi, second only to Mace.
Book 2: Inferno
War between the New and True Jedi. Not too much significant happenings, until, at the very end of the book, when Mace finds, buried in the depths of Palpatine's old files, the droid deactivation codes. Order 66 all over again, the surviving Jedi return to the Maw. Most are killed, but Anakin and Obi-Wan survive. Mace declares himself Emperor, with the New Jedi serving him, and the Senate executed. (cause why not)
Book 3: Gamble
23 years after "Inferno," the Death Star is completed, and Mace decides to make a huge gamble. Bringing himself, Maul, and much of his high ranking people onto the Death Star, he spreads rumors that the Death Star is going to destroy Mon Cala. (This has been a troublesome planet, with plenty of resistance.) Rebel operations have been very secret, the True Jedi have been simply waiting idly in the Maw. Anakin has trained Luke, and Obi-Wan has trained Leia. Everybody knows it's a trap, but considers it their best chance to strike. Mace and Maul know the risks as well, but also see it as their best chance to bring the True Jedi out of hiding and crush Rebel operations once and for all. Boba Fett joins the attack, still angry at Mace because of Jango's death. The True Jedi attack with plans to sabotage, and basically I write around ten chapters of utter chaos. In the end: Mace and Maul survive, the Death Star is destroyed. Mon Cala is destroyed as well. Anakin, Obi-Wan, Luke, and about half the random Jed survive. Leia is captured. The other half of the random Jedi are killed. Finding Maul old and incompetent, Mace wants a new apprentice in Leia. She, however, is very strong willed and does not succumb at all to the Dark Side. Mace feels Luke might be a better option. Luke can feel Leia's pain as she is tortured by Mace, but Anakin tells him that it is foolish to attempt a rescue. Luke runs off anyway. (The parallels are real) Luke fails miserably, but finds himself taken to a remote fortress, where he is held prisoner by none other than... Maul. Maul reveals that he wishes to overthrow Mace and rule, and he feels Luke might be a good ally. Luke agrees, and they plan to rescue Leia, then have the three of them kill Mace. Since the strongest rule, they would earn the throne. Maul trains Luke in the Dark Side, telling him that it is necessary. Luke realizes that he is more powerful, and accepts the training. They do indeed rescue Leia, but she immediately chastises Luke, realizing that he has fallen to the Dark Side. Things escalate, and Luke eventually battles and kills Leia. Once he finishes dealing with Leia, he finds Maul dead at Mace's hands. (Mace arrived unnoticed during their battle) Mace reveals that Maul served him the entire time, but that now Maul has served his purpose. Having killed Leia, Luke believes the Jedi would not welcome him back, and joins Mace. Luke and Mace go to hunt down Anakin and Obi-Wan in the Maw. Mace battles Obi-Wan, and Luke battles Anakin. They separate, each duo moving into a separate part of the ship. Both battle with words. Mace easily overwhelms Kenobi once the old Jedi fails to sway him back. Luke is defeated by Anakin, but Anakin believes that killing Luke would bring him to the Dark Side. Anakin, using an old ritual, separates himself from the Force and runs away from the Maw. He lives his remaining days as a sad hermit, before eventually dying of old age. Mace rules with Luke at his side.
I know Inferno doesn't have a lot of "meat" to it, but I hope you enjoyed finding out what was going to happen.