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. – Lobo 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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