Disclaimer: I own no part of the Star Wars franchise.
Darth Sidious looked at the wreckage of the room following his confrontation with four Jedi Masters. It had been far too close, only his careful grooming of Anakin Skywalker had saved the Sith Master from Mace Windu. His new apprentice was now on his way to the Jedi Temple to deal with the "younglings."
"Well, it seems that the Jedi have become a threat to the galaxy," he said, mostly to himself, "time to end this."
Palpatine moved to his communication centre and went through the process required to activate Order 66. Once he had finished he leaned back in his chair, visions of Jedi dying at the hands of their trusted Clone Troopers delighting him.
"Well, aren't you full of yourself?" a voice said from across the room. Palpatine spun around in his chair to see a middle aged female human dressed as a Jedi Master.
"Who are you?" the Sith Master demanded, not recognizing this particular Jedi. After all this time he thought he knew all of them.
The woman raised an eyebrow. "My name is of no consequence, at least to you. The more pertinent question for you is - why am I here?"
Palpatine's eyes narrowed. "That had crossed my mind. I have already dispatched four Jedi Masters today, are you here to be the fifth?"
The woman smiled mockingly. "I noticed that you needed help for that fourth Master, or are you in the habit of using Force Lightning on yourself? Besides, I am not so foolish as to confront a Sith of your skill by myself."
"Quite," another voice, this one apparently from a male human, said from behind Palpatine, "we have been preparing for this for some time."
Palpatine hastily looked behind him, only to discover that he was now surrounded by more than a dozen beings dressed as Jedi Masters.
"I must say that you are one of the more devious Sith we've seen for a while," the woman who had first spoken went on, "infiltrating the Republic via the democratic process requires more patience than the average Sith has. Such a shame for you that you and your Master weren't nearly as clever as you thought."
Palpatine snarled as he turned back around to face the woman. "So, you would have me believe that you've been watching me this whole time? Please, if you had known about me I would never have made it this far."
"That's where you are mistaken," the woman replied with a smile that didn't reach her eyes, "we are not of the main Jedi Order. We are the watchers in the dark, the Jedi who take the long view. We found out about your plans back when you were still just a student, but it suited our purposes to let you proceed."
The Sith Master laughed once, sharply. "I doubt that. Jedi allowing a war to be fomented? Permitting the deaths of how many billions? You are too soft to even think about such a state of affairs, let alone allow it to occur."
"And that's where you are only partially correct," the woman stated evenly, "certainly none of the current Jedi Council members would even contemplate allowing all of your plans to be carried out. But we, as I said, take the long view. And long before you started your rise to power, we could see that the Galaxy was becoming corrupt.
"The Republic became far too complacent and the Jedi Order too wedded to the government. Corruption of the political process was overlooked by the Order, while generations of politicians became used to the Jedi saving them from their own failings. It was well past time for the galaxy to be reminded why the Jedi Order is important, just as it was also important that the Order be reminded why it should not allow itself to be made a tool of the government."
Palpatine stared. The implications were shocking.
The woman smiled again. "So we let you manufacture this war. We let the Order go into battle ignorant of your plans. We allowed the Republic to be turned into a military dictatorship. Because it will serve as a useful object lesson."
"Such a shame that you've let it go too long," Palpatine said, sneering, "even as I speak your precious Order is being destroyed."
"If you mean Order 66, we changed that years ago," the woman replied, "those Clone Troopers are solely loyal to the Jedi. Which means that all you've done is give the Order an army. And as for young Anakin, well, he will find that the 501st Legion will be unwilling to attack the Jedi Temple. He will also find a number of my colleagues waiting to take him into custody...or kill him, if it comes to that."
"I cannot believe this," Palpatine hissed, "no Jedi could be so coldly calculating and stay true to the Light Side."
"It is hard," the woman admitted, "but as I said, we take the long view. From a certain point of view, a bit of blood shed now will save a lot more blood shed later on. That attitude has meant that we have been a secret part of the Order for thousands of years, so secret that even the Council was not aware of our existence. And thanks to that secrecy..."
More than a dozen lightsabers ignited simultaneously.
"...you have to be kept quiet."
Author's Notes: the basic idea is that there has always been a covert branch of the Jedi Order that is quite Machiavellian in its approach, a branch the rest of the Order is kept ignorant of. They allowed Palpatine's plans to proceed for much the same reason that Ozymandias created a disaster/crisis in "Watchmen."
As for the "evil villain" exposition - well, even Jedi can enjoy a bit of schadenfreude, especially when their Xanatos Gambit comes to fruition.
Regarding my other writing - I ran into a monster writing block on "Circle of Light" but I'm working my way through it. Sorry about the lack of updates.