The story starts 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 to push back the Separatist Droid Army, under the command of Count Dooku and Grievous and the Sith forces, including Darth Maul, Asajj Ventress and the battle droids start an all out retreat. All of a sudden, the young Padawans come to the aid of Yoda, C-3PO and R2-D2 and together they 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 that 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.
On Mustafar Dooku, Grievous and 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 to make fun of their teacher, pointing out that Dooku's name rhymes with Doodu, to which Darth Maul adds, that the Sith are vicious and vengeful, but that they are not rude, but the Badawans trick him into checking his wrist watch, burning his lightsaber in the process. What the Sith don't know, is that commander Cody was spying on them and reported their location to the Jedi.
Meanwhile the Senators on Coruscant are debating, where the WE'VE WON THE WAR PARTY should take place, when the Jedi inform the Senators and Chancellor Palpatine, that the Sith are on Mustafar and that they should mount a surprise attack against them. Palpatine agrees and orders every Jedi to be sent to Mustafar, to mount an ambush against the Jedi. Latter, in his office, Palpatine tells the happenings to Dooku. When Palpatine asks if the Badawans are ready, Dooku adds that they are a handful, but that the new Disciplinary Officer Poggle the Lesser will deal with them. Things not go according the plan, as Poggle's mother tongue is made fun of by the Badawans, because of its relation to popping and toilet humor sounds. Palpatine is not amused and orders Dooku to wait for him. 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, to his dismay.
Back on Mustafar, Dooku has prepared a welcome party for his master, and threatens his students that Darth Sidious, the "evilest man ever" is coming to teach them a lesson. After waiting several "minutes" for his master Dooku becomes nervous and sends Grievous to find him.
Meanwhile in orbit above Coruscant, the fleet is ready to depart to Mustafar. As Anakin says that 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 addressed by Lord Sidious and then even appears with his ship beside them, to the dismay of the crew, especially the Chancellor, who panics and denies him knowing who Grievous is. The Jedi start to chase after Grievous, but he manages to escape, when all of the Republic ships collide. With all but one of the Republic ships in ruins, the Chancellor, the 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 help them, 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 his annoyance.
Meanwhile Grievous is talking with Dooku through a holographic image when Dooku orders him back to Mustafar, but when Grievous sees what the Badawans are doing he decides, that he will keep looking for their Sith commander, 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 when he has to listen to the Ewok song. He snaps and makes up the story, that he is allergic to Ewok fur. He steals Jek's ship, leaving C-3PO behind, but get's blasted by Grievous who mistakes him for Jek.
Back over Coruscant the Jedi thank Jek for saving them and depart. Jek feels conflicted if he should help the younglings. After much debate he decides that they need his help and departs for Mustafar.
Back on Mustafar, Sidious and Grievous arrive in Grievous' Starfighter and Sidious quickly manages to whip the Badawans into shape after electrocuting them. Sidious tries to prepare the Sith for the battle against the Jedi, not knowing that their ships are landing. When he finally realizes what is happening he quickly transforms into Palpatine and orders the Jedi to attack them. A fierce battle rages loose between the Jedi and the Sith and the Jedi start winning as the Sith start to retreat. 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 after the Badawans mock him, so he destroys the Klegger Corp Mining Facility and repairs the Jedi ship.
When the Jedi arrive to Coruscant the Padawans throw a party for Jek. Everyone cheers and has fun, except for Palpatine who sobs at the podium. He gets into a better mood when he sees Anakin Skywalker sobbing as well, as no one is congratulating him, even if he is the chosen one. Palpatine cheers Anakin up and slowly starts regaining his trust, as his future Sith apprentice.
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