The story begins on Geonosis, where a battle between the Jedi and the Sith wages on. With the help of Yoda, the Grand Army of the Republic gains momentum and slowly starts pushing back the Separatist Droid Army, which is under the command of Count Dooku, Grievous and the Sith forces, including Darth Maul, Asajj Ventress, causing the battle droids to retreat. During this time, the young Padawans come to the aid of Yoda, C-3PO and R2-D2, helping them to defeat the separatist leadership. After the battle, Anakin Skywalker asks Yoda if he knows the consequences of the successful battle on Geonosis, to which Yoda replies he does, and that the answer is a "medal ceremony."
Back on Coruscant, the medal ceremony takes place, to which Palpatine sadly replies that the Sith have been thwarted once again by "four children, two droids and an 800 year old green guy," quietly adding that "life isn't fair," while everyone else cheers.
Now back on Mustafar, Dooku, Grievous, the other Sith Lords and followers have established a new plan: to open a Dark Padawan Academy for the Dark "Badawans." The Badawans immediately start poking fun at their teacher, pointing out that Dooku's name rhymes with doo-doo. Darth Maul interjects and tells the students that the Sith are vicious and vengeful, but that they are not rude; however, the Badawans trick him into checking his wristwatch, causing ignition of his lightsaber in the process. What the Sith don't realize is that Commander Cody was spying on them and reported their location back to the Jedi.
Back on Coruscant, while the members of the senate are debating where the 'WE'VE WON THE WAR PARTY' should be held, the Jedi inform them, along with Chancellor Palpatine, that the Sith are on Mustafar and suggest mounting a surprise attack against them. Palpatine agrees, ordering every Jedi to Mustafar in the hopes that the ambush will lead to the Jedis' demise. Later in his office, Palpatine conveys the happenings to Dooku. When Palpatine asks if the Badawans are ready, Dooku informs his master that they are a handful, but that the new Disciplinary Officer Poggle the Lesser will deal with them. However, things do not go according to plan, as Poggle's mother tongue is made fun of by the Badawans because of its relation to popping and toilet humor sounds. Palpatine, not amused, orders Dooku to wait for his arrival. His plans are almost thwarted as he almost reveals his true identity to the Jedi. The Jedi decide to go with Palpatine in order to guard him and keep him safe, much to the Chancellor's dismay.
Back on Mustafar, Dooku has prepared a welcome party for his master, telling the Badawans that the "evilest man ever" is coming to teach them a lesson. After waiting several "minutes" for Palpatine to arrive, Dooku becomes nervous and sends Grievous to find him.
While in orbit above Coruscant, the Republic fleet is ready to depart and travel to Mustafar. As Anakin says, "This is the day the Sith will finally be conquered," Palpatine tries to reason the acts of the Sith to the disbelief of his fellow crew members. His plans are almost thwarted when he is contacted by Grievous, who addresses him by Lord Sidious while in the presence of Republic crew members, causing Palpatine to vehemently deny knowing who Grievous is. The Jedi begin to chase Grievous, but he manages to escape when all of the Republic ships collide. With all but one of the Republic ships destroyed, the Chancellor, Padawans, C-3PO and Yoda depart for Endor, where the only person who can help them, Jek-14, is staying. At first, Jek is reluctant to assist, but with help of some childish charms he agrees. The Jedi and Jek depart for the ruins of the fleet, while Palpatine is stuck on the planet with C-3PO, to the Chancellor's annoyance.
While Grievous is talking with Dooku through a holographic image, the Count orders him back to Mustafar; however, Grievous, seeing what the Badawans are doing, decides he will keep looking for their Sith commander, much to the dismay of Dooku.
Back above Coruscant, Jek easily repairs the Republic fleet, assembling all the ships into one large vessel. Back on Endor, Palpatine is going through torture while listening to the Ewok song. He snaps, stealing Jek's ship, and leaving C-3PO behind in the process; however, his ship is shot down by Grievous who mistakes Palpatine for Jek.
Back over Coruscant, the Jedi thank Jek for his invaluable assistance and depart. Jek feels conflicted, wondering if he should help the younglings. After much internal debate, he decides to aide the younglings and immediately heads to Mustafar.
On Mustafar, Sidious and Grievous arrive in Grievous' star-fighter and the Sith Lord quickly manages to whip the Badawans into shape by electrocuting them. Sidious tries to prepare the Sith for the battle against the Jedi, not knowing their ships are landing. Finally realizing what is happening, he quickly transforms into Palpatine and orders the Jedi to attack the Sith. A fierce battle breaks loose between the Jedi and Sith; the Jedi deploy a squad of Clones, but they are quickly wiped out when the Sith ambush them from behind. Meanwhile, Palpatine throws a grenade on the Jedi ship, destroying it. The Sith now advance and are on the brink of victory when Jek arrives and defeats the Sith. The Jedi and Republic soldiers head back to Coruscant.
When the Jedi arrive back home, the Padawans throw a party for Jek. Everyone cheers loudly except for Palpatine, who sobs at the podium. He gets into a better mood when he sees Anakin Skywalker sobbing as well, due to no one is congratulating him, even if he is the Chosen One. Palpatine cheers Anakin up and slowly starts regaining his trust, believing he can make the young Jedi his future Sith apprentice.