Vader watches Shaak Ti struggle to internalize everything he's told her so far. It's certainly a lot to take in at one time, but even worse still when you don't have all the answers. And she doesn't have nearly enough answers to understand. The question then becomes just how much to tell her.
Despite their… copulation, he doesn't think she's ready to hear that he himself is a Sith just yet, or about his future plans for the galaxy. Ahsoka was one thing, still quite malleable and perfect for transitioning from Jedi Padawan to Sith Apprentice. Grievous and Asajj, meanwhile, needed to know they were dealing with a Sith and not a Jedi, or they never would have signed on.
Shaak Ti was the opposite. She might be Fallen, but she was still a Jedi Master. She was still rigid in a way that it would take quite some time to unwind. Only once the Togruta Jedi Master was properly flexible and elastic could Vader give her more information about him personally.
At the same time, she needed to know some things if she was going to be of use to him going forward. He'd come to Kamino to do more than just recruit Ventress after all, but now he saw an opportunity to leave an ally behind when he inevitably has to leave after he's done. And if he's going to make sure Shaak Ti's loyalty is unassailable, she'll need to know at least some things. Like for instance…
"You question what purpose they truly serve? Simple, really. I'm sure you've read Master Kenobi's report on his conversation with Jango Fett."
Shaak Ti nods hesitantly. Not every member of the High Council would have been up to date on such a thing despite all of them having access. But Vader knew Shaak Ti would be one of the ones who was, simply because of her attachment to the clones.
She would have consumed every bit of information she could find even tangentially connected to them. And Jango Fett's conversation with Obi-Wan Kenobi was a bit more than tangentially connected to the Clone Army's existence.
Vader sees the moment that Shaak Ti catches up, her mouth opening in shock and her eyes widening in horror.
"Tyranus… Fett said that he was hired by a man named Tyranus, not Sifo-Diyas. Who is this Tyranus, exactly?"
Smiling thinly, Vader steps forward and brings a hand up to Shaak Ti's cheek. Her breath hitches but he's not trying to restart their physical intimacy or anything like that. Instead… he helps her truly see.
"Use the Force. The Jedi might have been blinded by the Dark Side for over a decade now, but you are no Jedi, not anymore. The Dark Side is no longer your enemy, it's your ally. Reach out and search using your feelings. Discover the truth."
The Togruta leans into his touch, shuddering a bit as her eyes flicker Sith Yellow while she tries to do what he's bid her to. She wouldn't manage it without him helping her out of course, but Vader nevertheless takes a gentle approach in leading her to the information she seeks.
Until finally, Shaak Ti gasps, her eyes snapping wide open from how lidded they'd gotten in her state of concentration.
"Dooku. Tyranus is Count Dooku."
Vader smiles, pleased to see Shaak Ti reach that conclusion on her own. The Force is a powerful tool for discovering the truth of such things. But the Jedi Order has been cut off from methods like that for a while now as the Force became more and more clouded by the Dark Side Shroud that Sidious even now maintains.
Even a Jedi Master like Shaak Ti doesn't think to try and use the Force for such things anymore. Only on a localized scale at best, but never anything so grand as what she just did. And yet, through her connection to the Dark Side, anything is possible… with Vader's help of course.
"B-But… that would mean the Clone Army was created by the Sith. I don't understand… why would they do that? Why would they give us and the Republic an army of slaves to do our bidding?"
Vader raises an eyebrow at that, but it seems Shaak Ti needs the nudge. She's still blind in some ways.
"Tell me Master Ti… do you know how many Jedi have died since the Clone Wars started? Not even counting the massacre on Geonosis. How many Jedi have fallen on battlefields they had no place being? Masters, Knights, Padawans. High Generals, Generals, Commanders."
Shaak Ti's eyes get progressively wider as she finally understands what he's saying.
"… They're bleeding us dry. And not just that either. They've perverted our purpose too. How many more have Fallen like you and I? They've given us the tools to… to destroy ourselves."
Vader smiles grimly.
"Yes. But that's not all."
Twitching, Shaak Ti narrows her eyes.
"What do you mean that's not all? I… I sense that I'm really, really not going to like what you're about to tell me, Skywalker."
Inclining his head, Vader hums.
"No, you will not. Because the Sith aren't about to leave anything to chance. Dooku has his droid armies to lay waste to Jedi and Clones alike, but there's a chance the Order might eventually realize what's happening. They might figure out what's going on and decide to do something about it. The Sith can't let that happen though, obviously. Which is where Order Sixty-Six comes into play."
A full body shudder goes through Shaak Ti at that, her eyes widening as she looks at Vader.
"What… what was that? Those words just now… they had a metaphysical weight to them. The Force itself shivered at their utterance."
She's not wrong, but Vader just continues on.
"There are one hundred and fifty different contingency orders trained into the clones from birth. Hidden among them is the only one that matters… the one that the Sith have been waiting for the right moment to use since this war started. The more Jedi die on the field of battle, the more are sent to the frontlines, leaving the Temple emptier and emptier. In turn, this leaves more and more of the Order reliant not on their fellow Jedi, but on their Clone Troopers. Which is precisely what the Sith want."
Shaak Ti is hanging off his every word now, so Vader finally gets right to the point.
"Order Sixty-Six reads as such; In the event of Jedi Officers acting against the interests of the Republic, and after receiving specific orders verified as coming directly from the Supreme Commander, GAR Commanders will remove those Officers by Lethal Force, and command of the GAR will revert to the Supreme Commander until a new command structure is established."
The Togruta Jedi Master's mouth opens and closes a few times before she finally finds the words to respond.
"The… the Supreme Commander. That would be… Chancellor Palpatine, wouldn't it? So then Count Dooku was telling Master Kenobi the truth? There is a Sith Lord in the Chancellor's Office that has subverted both the Supreme Chancellor and the Senate?"
Vader shakes his head.
"You're not thinking big enough, Shaak Ti. Tell me… why would Supreme Chancellor Palpatine need to subvert himself?"
And there it is. The reveal causes quite the reaction as the Togruta Master stumbles back in shock. Vader just nods.
"Chancellor Palpatine is a Sith Lord. More than that, he's the Sith Master. Dooku is merely his apprentice. They're playing both sides, Shaak. The entire Separatist Movement is controlled opposition meant to distract from Palpatine grabbing more and more power. Until at long last, they're ready to take over."
Understanding dawning now, Shaak Ti slowly nods even as she grimaces.
"… At which point the Chancellor will tell the clones to execute Order Sixty-Six and the entire Jedi Order will die…"
She says it in a murmur, but almost immediately violently shakes her head.
"But… no! I refuse to believe that! The clones… they might be trained, but they are still thinking men! They have their own hopes, aspirations, and dreams! I've watched them training, I've watched them growing up. Just because the Supreme Chancellor gave an order doesn't mean they would follow it, surely!"
The look on her face is almost pleading now.
"I know… I know the Order has not done right by them anymore than the Republic has, but there are bonds being forged on battlefields all across the universe between Jedi and Clone alike! They wouldn't turn on us that easily! Not all of them at least… right?"
It was time to do what he'd come here for. Vader shakes his head and gestures.
"Get dressed and come with me."
Shaak Ti blinks but hastens to obey. There's a tenuous connection formed between them. Not quite a Master-Apprentice bond or anything like that, but their physical copulation had its consequences. And after everything, she's more inclined to follow his instructions anyways. He's already proven himself not just stronger than her, but also unequivocally on her side.
Eventually, she's dressed again and so is he. With that, Vader leads her out of the small chamber she's sequestered herself in and out into the greater area of the Embyro Room. The main hall is massive of course, as well as filled with Kaminoan Scientists and Technicians.
It takes Shaak Ti a moment to realize that none of them are paying the two of them any mind though. She gives respectful and cursory nods to the first few that they pass, only to finally catch on that for some reason, they're being ignored. Vader just smiles when she gives him a questioning look.
"My presence here must remain… understated. I was just checking in, not doing anything too… invasive. Our enemies would be especially upset if they found out I was looking into what I'm about to show you. Upset enough to make… unwise decisions."
Shaak Ti gets more worried AND more curious at that, even as they approach a station. Specifically, the station that oversees the third stage of every single clone trooper's embryonic development. There's a Kaminoan already there, but Vader waves them off with a simple push of the Force. The alien minds were actually fairly difficult to persuade with the Force for your average Jedi, but Vader hadn't been a Jedi for a long time now. And he'd never been average.
They stand in front of the control station together as Vader's hands dance across the controls while his technopathy ensures that no traces of their search will make their way to any… interested parties. Shaak Ti stands beside him, watching on curiously until at long last she jolts as something is brought up on the screen in front of them.
"What... what is that thing?"
Vader tilts his head to the side as gazes at what appears to be some sort of organism. Of course, it's so much more than that.
"The Kaminoans call them Behavioral Modification Biochips. But they've also been called inhibitor chips, control chips, and even behavioral inhibitor biochips."
"… No."
Vader nods as Shaak Ti gets it rather quickly.
"Oh yes. This is why the Sith do not worry about the bonds formed between the Jedi and their Clone Troopers. Because when the time comes for Sidious to execute Order Sixty-Six, these biochips will ensure that every single clone obeys without fail."
They would later be used on the Wookie Population of Kashyyyk during the reign of the Galactic Empire… or rather, they would have been. Needless to say, Vader had no intentions of letting that happen again. It was unfortunate, the role he'd played in the conquest of Kashyyyk the first time around. But he was a mere shell of his former self at that point… an efficient killing machine and little else.
Never again. Not while he still drew breath.
"This… this is monstrous. This cannot be allowed to continue."
Vader nods as he looks over to Shaak Ti.
"I'm glad we are in agreement. I will be putting a change in the system that I assure you will go unnoticed by everyone. It will ensure that going forward, the biochips inserted into all future clones will be defunct and inoperative from the start."
He expects Shaak Ti to protest that, to ask why they can't just make sure there are no more biochips at all. But she's smarter than that, Vader is pleased to note.
"Of course… we can't shut it all down completely, not without alerting the Sith. But… what about all of the clones already out there? There are millions of them, all with working biochips still in their heads."
Vader nods, smiling grimly.
"Indeed. Fortunately for us, the Kaminoans are an arrogant people. The Prime Minister Lama Su should still have access to the control chips at this point in time. I will be paying a visit to his office before I depart, where I will be tampering with the activation phrases of all current biochips."
Shaak Ti furrows her brow at that.
"I… I see. And what… what should I do? What can we do? Even if you're making sure that the Sith can't turn the clones against us, Count Dooku still has an innumerable amount of droids at his command. And Chancellor Palpatine still controls the Senate!"
"Indeed. Which is why we must move carefully. Even once we take control of the clones out of our enemies' hands, they will not be without power or options. To say nothing of how the Jedi Order and the Republic have failed to do anything in the face of the injustices visited upon the clones by the Kaminoans in the first place."
A shiver runs down Shaak Ti's spine and he feels her anger and hatred in the Force. As well as no small amount of self-loathing. Reaching out, Vader places his hands on her shoulders.
"That is why I need you to stay here on Kamino and make sure that they neither discover the changes to the new or old biochips, or manage to do anything else to these poor children they're creating. Can you do that for me, Shaak Ti?"
Straightening up, her eyes wide, Shaak Ti nevertheless nods.
"Yes. Yes, I can do that."
Vader smiles and nods back before letting her go.
"Good."
He turns back and finishes changing the biochip so that none of the new clones will be ticking time bombs like the current ones are. Truth be told, stopping creation of the clones altogether would be nice, but that can't happen just yet.
Finally, he leads Shaak Ti back to the small side chamber she'd been meditating in and stops shrouding her from the Kaminoans. Giving her one last nod, Vader shrouds himself from even her senses and begins making his way to Lama Su's office.
He hopes, when all is said and done and she learns of his true nature as well as his plans for the galaxy, that Shaak Ti will not set herself against him and Padme. But he's also not sure she's really Sith material.
Only time will tell, in the end…