in episode 3,lucas will have to put the events that bring obi-wan,bail organa and others to join the rebels.we know that the separatiste movements is a rebel movement agains the republic.i think that dooku will betray sidious and join back the jedi because of many reason.
1:dooku' apprentice,qui-gon have been killed by a sith.
2:dooku have been a jedi about 70years.
3:dooku's plan was to inflitrate the sith to defeat them by interior,at high cost.because of the inaction of the council and the senat to stop corruption in the senat.he was tired of that.
obi-wan will see that dooku as not lie when he told him that a sith was controling the senat.dooku will convince obi-wan to join him in the separatiste movement when all will know palpatine is a sith and the empire is born at the end of the film .
it could be one of the reason anakin battle obi-wan.when he'll see obi-wan allies with dooku,anakin will be furious to see is former master is a traitor of the republic,anakin who like palpatine.