*basically the one we all know from Season 6 of Clone Wars, in my Tales of the Clone Wars AU of course, but from a different POV.
The Jedi council now: Yoda, Mace Windu, Elizabeth Mareel, Plo Koon, Obi-Wan, Shaak Ti, Mira Wurhui, Anakin Skywalker, Shadday Potkin, Kit Fisto, Ki-Adi-Mundi, Etain Tur-Mukan.
*Ok, to explain. Anakin was promoted to the rank of master, and then granted a seat on the high council. Eeth Koth stepped down from his position on the council because of the guilt he felt for voting against Anakin during the 'judgement' by the council, and Etain was elected to the council not long afterwards. Ahsoka was knighted, and so now she has taken on a Padawan herself, choosing Katooni, you know, that girl youngling from the episode 'the gathering', and basically they get sent to Ringo Vinda with the 501st instead of Anakin. Yoda is still trying to finish up fixing the Jedi code, but the new code is almost done.
Anyway, on with the story. And idk the time jump, so let's just say it's a month later.
.
.
.
.
.
.
Opening: Conspiracy. As the Jedi still reel from the betrayal of Jedi knight Flora Vizsla, the Clone war rages on. As the Jedi seem to be slowly gaining a foothold over the planet of Ringo Vinda, Jedi knight Ahsoka Tano, alongside her new Padawan, Katooni, storm the droid defenses on board the circular station that surrounds the planet. Aided by twin sister Jedi masters Tiplee and Tiplar, the Republic mount a desperate offensive, to break the deadlock.
Meanwhile, the Jedi council moves to change the Jedi code, and to ensure the order itself, does not fall further.
.
.
.
.
.
Anakin sat in his seat in the council chambers, they were currently in debate about missions.
Separatist activity was picking up near Mygeeto and Felucia, but it wasn't a lot, yet, so they weren't too concerned yet with that.
They had dispatched Jedi masters Kento Marek and Rahm Kota to deal with CIS movements near Nar Shaddaa.
Rahm of course opting to take his militia instead of the clones, though Anakin would never understand why.
While Kento had been strangely reluctant at first, but ultimately gave in.
Regardless, they were on their assignment.
"Any word from Knight Tano?"
Plo turned to Mace and shook his head.
"Not as of yet."
"How do you think they're doing?"
"I imagine as well as they can do against a blockade."
Then a transmission from commander...Doom was it?
"Report, what have you?"
Yoda looked very curious to the sudden nature of this.
Doom nodded.
"Generals, there has been an incident."
Obi-Wan sighed.
"What has Ahsoka done?"
Anakin looked at him with false offense.
"Hey, why do you assume..."
"Given she learned from you, I think it's self explanatory."
Anakin chuckled.
"Fair enough I guess."
He shook his head.
"Sorry, seriously commander, what incident?"
Doom sighed deeply.
"Clone trooper Tup tried to kill commander Katooni."
The entire council went stiff. Anakin was worried, was his now former student's Padawan alright? Why had Tup tried to kill her?
"And Katooni?"
"She's alright, she only got grazed by the shot, shaken up other than that."
Obi-Wan nodded in understanding.
Elizabeth then asked what everyone was thinking.
"Why did Tup try to kill her?"
Doom shook his head.
"We can't figure it out either generals, Rex and Fives said he just kept uttering the phrase 'good soldiers follow orders'."
Anakin was lost.
"Good soldiers follow orders? What does that mean?"
Anakin was getting a very odd feeling about this just from repeating that phrase.
Mace nodded.
"Perhaps brainwashing?"
Shaak Ti disagreed though.
"How? He's been with the 501st the whole time, always accounted for, there's no way he could have been brainwashed."
Mace turned back to Doom's hologram.
"Thank you for reporting this commander, the council will look into this matter."
Doom nodded before his hologram disappeared.
Yoda hummed in thought.
"Disturbing, this news is."
Anakin nodded.
"Agreed master, but what are we going to do?"
Yoda went back into thought for a minute before turning to Shaak Ti.
"To Kamino, the council will send master Ti, and you, master Skywalker. Investigate this matter, you shall."
Anakin nodded, liking the idea. He felt better knowing Shaak Ti would be there, especially given her smart brain could figure out anything, in his opinion anyway.
"You got it master."
-----------------------------------------------------------
The two council members departed from the temple in a shuttle immediately after the council session ended.
During the ride through hyperspace, Anakin decided to ask.
"Master Ti, can I ask you something?"
She smiled.
"You may ask, I consider us friends Skywalker."
He nodded in thanks before continuing.
"How is Nicholas?"
He realized the question was stupid, obviously Nicholas was doing horribly.
Nicholas hadn't spoken to him since Flora's betrayal, clearly blaming himself for all of it like Anakin feared he would, and it made him despise Flora to the core.
Anakin had run into him in the halls once, but Nicholas had very nervously uttered an apology and walked off.
Shaak Ti had expressed to the council she was at a loss on what to do.
Nicholas was like a son to her, but she just didn't know how to help him.
Mace suggested he seek counsel from master and chief healer Valurha Osedh, but the council felt it wouldn't really work, so Yoda suggested they give him time to work this out himself, and they all, reluctantly, agreed on that.
Shaak Ti sighed.
"Like you'd expect. I think Elizabeth and Luminara said they caught him in his room crying constantly, just non-stop sobbing. I just...I don't know what to do."
Anakin gave her a sympathetic look.
"Just try to be there for him. Even if you can't do much, be a shoulder for him to cry on."
"I wish it were that simple. I have moments where I stop and start thinking the council should never have assigned Flora as his Padawan."
Anakin understood that but...
"To be fair, she wasn't corrupted by the dark side, at the time."
She nodded.
"True, but we should have seen something, anything."
Anakin frowned a bit.
"Some people are far better at hiding things."
She sighed in exhaustion.
"I suppose you're right."
.
.
.
.
.
Anakin did not realize just how true his statement was.
.
.
.
.
.
They eventually dropped out of hyperspace, and arrived at Kamino. They then landed and got off, then approached the kaminoan doctor Nala Se, who had two clone escorts.
"Master Jedi, I am glad to see you had a safe journey here. The clone in question has yet to arrive, but should be here soon."
Anakin nodded.
"Very good doctor, shall we go in?"
"Of course, follow me."
-----------------------------------------------------------
Turns out, Tup arrived not long after they had, accompanied by Rex and Fives.
Nala Se already took Tup to a room to be examined, while Rex and Fives both opted to stay.
Operations on Ringo Vinda went surprisingly better than expected.
Katooni had opted to help continue the fight, and she, Ahsoka, Tiplee, and Tiplar ultimately pushed through the droid defenses and made it to Trench.
The latter opted to not be taken prisoner, so attempted to shoot and kill Tiplar, only for Doom to open fire on him, killing him in the process.
At least they didn't have to worry about him anymore though.
Rex felt personally responsible for Tup's sudden...incident, and Fives was just concerned for his friend.
Nala Se had done multiple tests, but nothing so far.
"There does not seem to be any sign of infection in the blood, curious."
Shaak Ti shook her head and frowned.
"We must be missing something."
Anakin agreed, they definitely missed something here.
After this, a medical droid, AZI-3, suggested an atomic level brain scan, and the Jedi agreed, while Nala Se didn't.
So they spoke to the council.
"Currently we still have no answer to our problem. I am beginning to think brainwashing occurred though."
Mace looked at Shaak Ti in confusion.
"How could that be possible."
"We discovered that not long after arriving on Ringo Vinda, Tup was reported missing by Ahsoka, then after three rotations he turned up again. That event proceeded this episode."
Obi-Wan nodded.
"Your suggestion?"
"We would like to conduct an atomic level brain scan to see if his thought processes are still functioning normally."
Etain hummed.
"And what do the kaminoans think of that?"
"They feel Tup is so weak that such movements could potentially kill him, but ironically their approach is to terminate him, thus leaving his brain intact for the autopsy."
Shadday had an idea it seemed.
"Bring clone trooper Tup back to the Jedi temple."
Yoda nodded in agreement.
"Yes, examine him with the force we shall, and unravel this mystery, we will."
Anakin nodded, agreeing wholeheartedly with this.
"Yes master, we'll get Tup and bring him back immediately."
With that, they cut the transmission and went to their task.
They arrived back at the medical bay to find Rex about to stab Nala Se with a lethal injection.
Shaak Ti raised a hand.
"Stand down captain."
Fives just nodded to his own hand.
"Generals we have the evidence, it's right here!"
Anakin looked at Tup to notice a bacta patch on his head.
"Do the surgery without us?"
Rex nodded.
"With AZI-3's help sir, Tup will be fine, he's just unconscious."
Anakin nodded, as he gestured Fives over, and the latter handed him...was it a tumor?
A few clones came in after, but went back out per Nala Se's orders. Afterwards, they spoke to the Chancellor about this, who suggested they take it to the Grand Republic Medical facility.
For some reason, the force told Anakin not to trust that route, and he really didn't get why, but he ultimately felt the Jedi should examine it thoroughly first.
Later they spoke in the adjacent room.
Fives sighed.
"Sorry generals, we just wanted to help."
Anakin smiled a bit.
"No problem Fives, we understand your actions."
Nala Se frowned as she stared at the two clones.
"Perhaps we would know more by now if these clones had not taken matters into their own hands."
Rex frowned back.
"We only did what was best for Tup."
"Yet because of that, you will likely have killed him."
Shaak Ti motioned Rex to sit back down as she turned to the kaminoan.
"Doctor, there is no proof of your claim."
Anakin then placed the tumor in a case and picked it up and held it firmly in his left hand.
"We are delivering the tumor and Rex and Fives to the Jedi temple."
Nala Se frowned.
"The Chancellor said all data, and the tumor, was to go directly to the Grand Republic Medical facility on Coruscant, not the Jedi temple."
Shaak Ti shook her head, having Anakin's back.
"And it will get there, but after the Jedi have run an analysis on it first."
Nala Se scoffed.
"I protest, I must personally deliver the tumor to the Chancellor as ordered."
Shaak Ti turned to her again, but her glare was solid, and very piercing.
"You can protest all you want, my word is final."
The kaminoan doctor ultimately gave in, and the four exited the room, with Fives getting Tup on a stretcher behind them.
-----------------------------------------------------------
Nala wasted no time getting to the private communications room and contacting lord Tyranus.
Those Jedi were close, they couldn't find out about protocol 66, or everything would be for nought.
Tyranus spoke a bit displeased when called.
"Doctor, this had best be important."
"It is lord Tyranus, the Jedi masters Skywalker and Shaak Ti have discovered the chip, but not its true purpose, but they are about to depart and we cannot stop them."
Dooku frowned.
"How did this happen?"
"CT-7567 and CT-5555 conducted surgery on CT-7385, and found the chip, and proceeded to give it over to master Skywalker. The two Jedi plan to take it back to the Jedi temple."
Dooku hummed in thought.
"Hm, the Jedi can't be allowed to uncover clone protocol 66, or my master's plans will be ruined, and all our heads will roll."
However, then he grinned.
In truth, Dooku did not want to see the order's destruction, unlike his master who wanted to see its total annihilation.
However, this...this could be perfect. His master could be uncovered, soon, and he could help make sure it didn't happen, but then again there was such a thing as being clueless to what was happening.
He then grinned again.
"Let them go doctor."
"Lord Tyranus, I don't understand."
"Clone protocol 66 is no longer a necessary measure to have. For if the authority to issue it fell into the wrong hands, then the galaxy, including us, could be in for an unforeseeable future. Therefore, we allow the Jedi to discover it, and they will take care of anyone who dares use protocol 66 for their own nefarious purposes."
Nala Se truly didn't get it, she was completely lost now, but she knew it best to trust lord Tyranus judgement.
That and she didn't particularly like the Chancellor of the Republic, he gave her a very strange feeling of unease.
She nodded.
"Very well, lord Tyranus."
"One more thing."
She was confused but nodded.
"Be sure to make it to where only you and the prime minister of Kamino can issue the order, which will not be needed, but we must be safe with this."
She nodded, understanding his reasons for this.
"I will inform Lama Su immediately that no official in the Republic government no longer has jurisdiction to issue protocol 66, and that will now be left solely to the prime minister of Kamino and myself, but that its execution is no longer required."
With that, Dooku nodded, and grinned one final time.
Let's see what his master will do now.
*Yeah, I feel like Dooku wouldn't want the entire order wiped out, in contrast to Palpatine, and would rather like to see it reformed in all the right ways, granted he's not all there anymore, but he isn't purely evil, unlike a certain Chancellor.
Fr though, what do you think will happen now?