Rustizsword very good theory Sidious is indeed powerful because he wears the kyber crystal that makes him perhaps the most powerful force user of all time (No previous sith was stronger than him in fact he killed his master Darth Imperius. Dooku in the end probably betrayed Palpatine or before he could Palpatine sensed it (It's not easy to catch the old man off guard) but I digress Dooku was disgusted with the republi on which he blamed the death of Qui-Gonn and the complacency of the Jedi.
Dooku was I think a double traitor he set out to kill Sidious and in the end he was lured to the dark side while infiltrating with Sidioud. Yet he did not forget what he set out for. A spoiler says that at the beggining of EpIII Palps is held hostage by the separatists. Anyhow Skywalker shows up accompanied by Obi-Wan, Many Jedi (In starfighters, it's a space battle) and many clone trooper fighters. They infiltrate the flagship in which Dooku and Palps are in and Anakin kills Dooku (beheads him in case you're curious).