Menace of the Sith

Darth Sidious calls all Separatist leaders to Geonosis after the creation of the "Sith clone" named Jek-14, intending to reveal his latest weapon. As the Separatist leaders journey to Geonosis, a slight delay occurs because some of them must wait for Nute Gunray to finish his coffee. Once everyone is assembled in the Petranaki arena, Sidious informs the Separatists that the Clone Wars are not progressing favorably for them. He assures them that Jek-14, his new Sith weapon, will change the course of the war.

Jedi Obi-Wan Kenobi and Yoda have secretly infiltrated the Arena, disguised as Sith, unbeknownst to the Sith. The Separatist leaders are initially unimpressed with Jek, especially Gunray, who openly criticizes the clone, resulting in him being struck by Force lightning from Sidious. Jek then impresses the Separatist leaders with his demonstration of Force abilities. He obliterates several columns in the arena, destroys Nute Gunray's hat, and even forms a sign that reads 'GO SITH' using the debris. When Darth Maul complains that Jek appropriated his theme song, Asajj Ventress accuses him of acting like a diva.

At the Jedi Temple on Coruscant, C-3PO pleads with the Jedi Council to relieve him of his duties as a substitute teacher for the young Padawans, stating that they put him in great danger. The protocol droid adds that he is on the verge of an internal breakdown because of the stress. The Jedi agree and reassign him to Jedi Temple Food Services, which C-3PO appreciates. The Padawans receive a new instructor, Anakin Skywalker, who dislikes the idea of looking after Padawans. When the Padawans inquire about their destination, Anakin says that they are embarking on a journey of discovery to the frozen planet Hoth, which the Padawans dislike. Anakin attempts to persuade the students, but fails. The Togruta Padawan, Vaasa Ti, comments that he is a great Jedi but a terrible actor.

On Geonosis, Jek continues to impress the audience with his skills. Palpatine intends to create thousands of Jek clones and has Dooku present his new cloning machine. However, the test fails, resulting in Jek 15, a defective clone with only a fraction of his powers. Obi-Wan and Yoda reveal themselves, and a battle breaks out in the Arena. During the conflict, the Jedi defeat the majority of the Sith and their minions, but Sidious manages to escape. Obi-Wan remarks that the Sith is truly evil because he stole Palpatine's space gunship, to which Darth Maul responds that they just don't understand, but remains silent to protect Sidious' identity. Back on Hoth, Anakin takes the Padawans on a tour but is trampled by Tauntauns, much to their amusement.

Obi-Wan and Yoda are forced to fight Jek on Geonosis, and he easily defeats them. However, Jek refuses to execute the Jedi because they are unarmed, much to Dooku's disappointment. Jek considers himself neither Sith nor Jedi and decides to flee and be himself. Both the Jedi and Sith pursue him, but their ships are wrecked in the asteroid belt surrounding Geonosis. Jek then jumps into Hyperspace and says goodbye.

On Hoth, Anakin entertains the Padawans by giving them his prosthetic arm to play with, following C-3PO's advice, who states that he is always happy to assist and that Anakin should not be embarrassed. Meanwhile, at the Jedi Temple Restaurant, C-3PO is serving burgers when Cad Bane attacks him for not including light mayonnaise in his sandwich. C-3PO accidentally removes one of his breathing tubes from his head and reattaches them incorrectly. Bane becomes enraged and begins shooting at C-3PO, causing the droid to flee. As Cad Bane accidentally shoots at a fellow bounty hunter, a fight erupts in the restaurant.

Dooku and Grievous are traveling aboard the Separatist Subjugator-class heavy cruiser Malevolence. The Separatists are furious that none of the bounty hunters are willing to work for them after Jango Fett's death. Dooku orders Grievous to deploy several probe droids to locate Jek. Some of the droids arrive on Hoth, where Anakin expresses his frustration at not being able to join the hunt for Jek, believing that the other Jedi think he is not ready.

The Padawans leave Echo Base and find Jek creating beautiful ice sculptures in the snow. Jek admits that he does not want to fight but only wants to create and be left alone. Anakin attempts to attack Jek but is unable to penetrate the energy shield. Jek bids farewell to the Padawans and says that he must find a new home. Shortly after, Jek is attacked by probe droids and captured by General Grievous. R2-D2 awakens Anakin, who responds that he thinks he can be too impulsive at times.

Dooku and Grievous begin cloning Jek and head for Coruscant. On Coruscant, the Jedi Order debates their next course of action while Palpatine eavesdrops on them. Obi-Wan instructs Anakin to stay put, but he is already fighting the Separatists over Coruscant. Yoda argues that training Anakin was too risky, but Obi-Wan replies that it was Qui-Gon Jinn's final wish. Qui-Gon appears as a force ghost and tells Obi-Wan not to blame him for that. As the battle over Coruscant intensifies, Dooku creates several new Sith clones using Jek's genetic material. Unlike Jek-14, these Sith clones are loyal to the dark side and Count Dooku.

During the battle, Anakin's ship is destroyed by the Malevolence. While R2-D2 flies to Coruscant, Anakin and the Padawans use the Force to create new LEGO ships. R2-D2 lands in the Jedi Temple kitchen, where C-3PO is working, and destroys it in the process. After some difficulty, Anakin discovers the ship's "weak spot" and destroys the Malevolence, scattering its debris across Coruscant. At the Jedi Temple, the Padawans, the Jedi, and Palpatine cheer as the wreckage falls. Alternating between being Supreme Chancellor and Darth Sidious, Palpatine uses the Force to stop a large piece of wreckage carrying Dooku, Grievous, Jek-14, and the Sith clones from falling. He then immediately reverts to Supreme Chancellor as Yoda nearly uncovers his true identity.

Dooku presents an unconscious Jek before ordering his Sith clones to attack the Jedi. As the clones attack, Jek awakens and uses his Force powers to save the Jedi by destroying the Sith clones. He then uses the Force to throw Dooku and Grievous into the air. While Jek gains the affection of the Jedi, he tells them that he wants to be left alone and begs his new allies not to call him. Jek departs on his modified starfighter for an unknown destination.

The episode concludes with Yoda recording the memories of the mission in the Jedi Chronicles. He expresses pride in his Padawans' accomplishments and praises Anakin's valor, who will no longer be teaching the Padawans because C-3PO has requested the job again. Following a brief exchange, Obi-Wan pursues his master Qui-Gon Jinn's force ghost to discuss the matter of training Anakin.