Palpatine Still Betrays Dooku Palpatine would need to find both a new Sith apprentice and a new puppet ruler for the Separatists who'd keep the regime unified as well as Dooku did. While unlikely, Palpatine could use his Sidious identity publicly in this scenario and become the new face of the Separatists.
Palpatine never intended a victory for either side, after the Jedi figured out that he was the Sith puppet master and gave him an excuse to declare Order 66, the war was over with Sidious the only victor.
Both The Separatists & Republic Lost The Clone Wars
The Republic and the Separatists were manipulated into fighting the many battles of the Clone Wars, and both sides ended up losing. It seemed the Republic claimed victory after the Separatist council was killed, and their droid armies were shut down.
Originally Answered: Why did Palpatine/Darth Sidious want the Separatist dead? Because they were troublemakers. He intended them to be troublemakers, but once they served their purpose he didn't want them making trouble for him. Also, the defeat of the separatists burnished Palpatine's reputation.
Sidious, who secretly controlled the Separatist Alliance as part of his plot to take over the galaxy, had sent the Separatist Council to the volcanic planet Mustafar under the guise of protecting them, where their power collapsed after the Battle of Utapau.
During the slaughter scene, we see Anakin crying whilst killing the separatist. This is because Anakin is. not yet fully committed to the dark side. and has now realized through his actions.
Absolutely. Because he hadn't become that notorious cyborg yet, it was easy for the Separatist Leaders to notice something off about him. He had time to gasp, “You're—you're Anakin Skywalker!” before a fountain of blue-white plasma burned into his chest, curving through a loop that charred all three of his hearts.
Thus, while Qui-Gon was less powerful than the likes of Yoda and Mace Windu, Palpatine feared him more. In the simplest terms, he was a wild card, and with the Sidious executing an intricate decades-long plan to seize power and destroy the Jedi, a wild card was something he just couldn't afford.
Dooku believed that both the Jedi and Sith were corrupt and wanted to destroy them both. Dooku's vision for the Empire was to eliminate corruption and negotiate with Force users, but he was manipulated by Darth Sidious.
Obi-Wan tracked them to Geonosis, evading a fusillade of fire from the Fetts' starship Slave I. There, he discovered Jango was working with Count Dooku's Separatists.
As such, a Marshal Commander was roughly equivalent to a Major General or Lieutenant General in other services; it was also the highest rank a clone could be given in the Grand Army of the Republic.
But from Count Dooku's point of view, he believed that the cycle would continue and that one day he would dethrone Palpatine and take his spot. That only happens when an apprentice feels strong enough to challenge their master, and it's possible Dooku felt this during Star Wars: Attack of the Clones.
If Rey struck him down, Palpatine's spirit would pass into her, allowing the Sith to be reborn. Rey resisted him with the help of Ben, who'd returned to the light. But their defiance gave Sidious a new opportunity – he would drain the energy of their Force dyad to restore his own body, then rule alone.
Sidious was able to mask himself very well. Usually, Chancellor Palpatine didn't really meet with the Separatist Leaders. Only Sidious did. The Separatists—like Nute Gunray and the others—knew of Darth Sidious only.
From the moment Palpatine began to plot his takeover, nothing he did was out of the goodness of his heart. Everything would transpire in a way that would give him power, and any niceties were a way to fool his enemies into underestimating him.
Like her then-mentor Anakin Skywalker, Ahsoka initially respected Palpatine. Though the Chancellor ignored the young Padawan in their first meeting, bringing Skywalker alone into his office. Eventually, the two became enemies after Palpatine oversaw Ahsoka's trial, which ended with her leaving the Jedi Order.
While they might have been skeptical during the very first few missions they had with Anakin (which we are not shown), they quickly start trusting his judgement. When we see him command the 501st in the Battle of Christophsis, Anakin's clone troopers trust him implicitly.
Darth Vader's true identity as Anakin Skywalker was a highly guarded secret, known only to a select few individuals including Palpatine, Obi-Wan Kenobi, Luke, Han, Leia, R2-D2, C-3PO, Master Yoda, Bail Organa, Ahsoka Tano, Darth Maul, Grand Moff Tarkin, Grand Admiral Thrawn, Jocasta Nu, Ferren Barr, Verla, Reva, ...
Darth Vader acts like he doesn't even know C-3PO or R2D2. They were with him since he was a child. He did everything he could to forget his past. Also, his plating had been replaced many times, and protocol droids all look very similar.
