Palpatines Armies
I think Palpatine will control both sides of the Clone Wars. He will create the Mandalore Clones and start invading planets. To combat this, Palpatine as Chancellor will put forward the idea of a Clone Imperial Army to fight them. He will control both sides. Obi-Wan and the other Jedi of course will be on the Empires side, until they find out what is happening. Amidala will be in charge of the Imperial Army. In the script for TPM or the book there was a passage where Anakin told her that he had a dream where he saw her "leading a treacherous army into battle". Palpatine will start a galactic war where he controls both sides.