In Clone Wars Season 4, episodes 15-18, there is a whole plot about Count Dooku selecting bounty hunters for a mission to kidnap Palpatine from Naboo's Festival of Light. One of the bounty hunters is Obi-Wan Kenobi working under disguise, and in the end he foils Count's plan with the help of other Jedi .

Dooku did explain to his accomplices that he wants to blackmail Republic with Chancellor as his captive. But, as we all know, both Dooku and Palpatine are Sith. Therefore, they must have an ulterior motive for this complex operation, but this is never shown in cartoon. What could it be ?

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    To set up the opening set piece of Revenge of the Sith – Buzz Nov 22 '17 at 21:06
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    Why fight a big war at all when both sides are under your control? Well, they were obviously fooling people. – Umbrella Corporation Nov 22 '17 at 22:46
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    Because Dooku and Palpatine are both playing for the crowd. That includes pretending to try to capture or kill the other. – Valorum Nov 23 '17 at 0:36
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    @Bat Operation was too complex. First some bounty hunters had to be freed from jail, then they selected five among them killing rest, and then they started job itself with Dooku probably knowing that one bounty hunter is actually Kenobi. – rs.29 Nov 23 '17 at 1:27

While we, the audience, understand the link between Dooku and Palpatine, nobody in-universe does. Palpatine's ulterior motive was to continue to chip away at the behemoth that was the Republic and continue to gain more power for himself by creating situations that would induce fear into the population. He was also trying to spread the Jedi out and thin their ranks as much as possible before executing Order 66. Palpatine was (supposedly) always in control of the situation and was coordinating both sides of the war like a giant chess match that ultimately benefited him and the Sith.

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Classic False Flag. Dooku's people come close but not quite close enough to capture Palpatine--as a Sith, Palpatine was quite capable of assuring his own survival against some bounty hunters. The near miss, ideally with some friendly casualties, does three things. First, it creates fear. After all, if Dooku could get someone that close to the well-guarded Chancellor, is anyone really safe? Second, it creates sympathy for Palpatine. Look how well that brave man is holding up after his life was threatened! Such dedication as continuing to do his job despite the risks!

Third, and finally, if anyone did have even the slightest bit of suspicion about Papa Palps, they'd have the same question you posed. Why would Dooku try to capture the Chancellor if they were really working together? Clearly, an absurd notion.

From Dooku's side, and remember, they don't know he's working with Palpatine either, he's clearly doing his best to win the war. Shame about those bounty hunters screwing up and the Chancellor barely escaping, but that's not Dooku's fault. Just bad luck. Better luck next time!

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