To refrain from being thrown out of the Academy, five clone cadets must learn to work together and realize their future as soldiers of the Republic.

The Grand Clone Army of the Republic, led by Jedi Masters Yoda, Mace Windu, Obi-Wan Kenobi and other Masters must fight the New Droid Army of the Separatists to defend the Republic and the political stability of the galaxy.

It is three years after the Clone Wars. The leader of the droid army, General Grievous, has captured Chancellor Palpatine on board his ship, the Invisible Hand. Jedi Master Obi-Wan Kenobi and Jedi Knight Anakin Skywalker must fly through Coruscant safely, and enter the Invisible Hand so that they can rescue the captive Chancellor. Just when Palpatine is about to be released, Count Dooku shows up. Obi-Wan and Anakin both battle it out with him, but Obi-Wan ends up unconscious. Anakin slices off his head and kills him. Anakin carries Obi-Wan, and Palpatine follows him. They meet General Grievous face to face, and Anakin tries to fly the last half of the ship so that they can safely land on Coruscant. Later, Palpatine starts acting strange, constantly manipulating Anakin into believing that the Jedi Council is against him. Eventually, it is found out that he is the Dark Lord of the Sith. Jedi Master Mace Windu fights him...

The Grand Clone Army of the Republic, led by Jedi Masters Yoda, Mace Windu, Obi-Wan Kenobi and other Masters must fight the New Droid Army of the Separatists to defend the Republic and the political stability of the galaxy.