The game is Strategy Based, and is a Spinoff based on Star Wars: Republic Commando. The game has five levels, split into three sublevels.
Order 66 has been sent out to every Clone Trooper to kill their Jedi Masters. Delta Squad initially refuses, but the Chancellor vetoes their decision. On Cato Neimodia, they kill Jedi Master Plo Koon, and are given the location of their next objective. This happened to be on Mygeeto, where they were to eliminate Master Ki-Adi Mundi, and killed him after he threw his lightsaber. After failing to kill Obi-Wan Kenobi on Utapau, they are sent to Kashyyyk to kill Luminara Unduli and Yoda, but Yoda escapes from the chaos. They are then deployed to assist in the massacre of Jedi in Operation: Knightfall in the Coruscant Jedi Temple.