You are clone commandos that have shipped out with master Yoda and two young Jedi knights to the planet Kashyyyk to help the Wookiees defend their home from the Separatist Army. The battle is going well and the droid army is near the braking point when all the clones receive a directive directly from the Chancellor to execute Order 66. Compelled by your conditioning, you do what must be done and turn on your Jedi comrades.