Dooku was working for Darth Sidious

The shuttle whose landing lights had caught Jedi Master Obi-Wan Kenobi's attention on Cato Neimoidia carried more than Intelligence analysts and technicians. Grand Master Yoda was aboard, eager to see for himself what Obi-Wan and Jedi Knight Anakin Skywalker had discovered. The technicians had succeeded in inducing the mechno-chair's holoprojector to replay the image of Sith Lord Darth Sidious, and Republic cryptographers working with the Jedi were confident that the unique device would yield even greater secrets once it was relocated to Coruscant and examined thoroughly.

Refusing to let the mechno-chair out of his sight, Anakin had demanded to overseew its transfer to the waiting shuttle. Feeling unnecessary, Obi-Wan and Yoda decided to take a stroll down the corridor of Viceroy Nute Gunray's now appropriated palace. The venerable Jedi Master was pensive as they walked, the silence broiken only by the sounds of distant blasterfire and the tick, tick of Yoda's gimer stick as it struck the polished floor.

Obi-Wan wasn't sure if Yoda was pondering the image of Sidious, or the fact that two Jedi had been killed during the fighting on Cato Neimoidia. Every day saw more Jedi die. Many were as shot up as the clone troopers. Wounded, blinded, scarred, deprived of arms and legs...patched up by bota and bacta. More than a thousand Padawans had lost their Masters; more than a thousand Masters, their Padawans. When Jedi gathered now they talked not about the Force, but about their military campaigns. New lightsabers were constructed not as a meditative exercises, but to handle the rigors of close combat.

Reaching the end of the long corridor, Obi-Wan and Yoda turned and started back. Without taking his eyes from the floor, Yoda said: "Found something important, you have, Obi-Wan. That Count Dooku is in league with someone, proof this is. That in this war a greater part the Sith play than we realize."

The name Sidious had come up only once since the war began--on Geonosis, when Dooku had told an imprisoned Obi-Wan that a Sith Lord by that name had hundreds of Republic Senators under his influence. At the time, Obi-Wan assumed that Dooku was lying, in order to persuade Obi-Wan that he was still aligned with the Jedi, although attempting to thwart the powers of the dark side by his own methods. And yet, even after Dooku had revealed himself to be Sith-trained, Yoda and others on the Council continued to believe that he had been lying about Sidious. Two Jedi Council members were convinced that Dooku was the Dark Lord, having somehow tutored himself--by Sith Holocron, perhaps--in the use of dark side powers.

Now that Sidious appeared to be real, Obi-Wan didn't know what to think.

A hunt for Dooku's Sith allies had been going on almost since the start of the war. Dooku was known to have trained Jedi in the dark arts--Jedi Knights who had lost faith in the ideals of the Republic, Padawans fascinated by the power of the dark side, misinformed novices such as Asajj Ventress, who had been mentored by a Jedi--but the question remained, who, if anyone, had been Dooku's teacher?

Thirteen years earlier, when Obi-Wan had fought and killed a Sith on Naboo, had he killed a Master or an apprentice? The question was rooted in the belief that the Sith, having essentially defeated themselves a millennium earlier, had learned that an army of Sith could never stand, and that there should be only two at any given time. lest a pair of apprentices conspire to combine their strengths to eliminate a Master.

More a doctrine than a rule; but a doctrine that had managed to keep the Sith order alive, if well concealed, for going on a thousand years.

But the horned and tattooed Sith whom Obi-Wan killed could not have trained Dooku, because Dooku had still been a member of the Jedi Order then. As clouded as the dark side made some things, there was simply no way Dooku could have been living a double life within the walls of the Jedi Temple itself.