After escaping Jedi Master Yoda, Count Dooku and General Grievous have traveled to Kamino to start experimenting with creating a Sith clone army. Dooku approaches a pair of Clone troopers guarding a cloning chamber and use the Force to knock members unconscious. Meanwhile at the Jedi Temple on Coruscant, Yoda senses a disturbance in the Force while teaching the Padawans how to handle a rancor.

Back at the Jedi Temple on Coruscant, Jedi Master Yoda is teaching the Padawans how to destroy a Corporate Alliance tank droid when he feels a disturbance in the Force. Count Dooku and General Grievous have captured a Clone trooper.

During the Great Jedi Purge, Emperor Palpatine's Clone troopers attack the Jedi Temple on Coruscant. As the Jedi Purge rages, Palpatine remarks that this is his best birthday ever. On Kashyyyk, Jedi Master Yoda and the Wookiees flee several Clone scout troopers intent on executing Order 66. Yoda manages to commandeer an AT-RT walker and warns Obi-Wan Kenobi that the Clone army has turned on them.

As the Old Republic falls, Jedi Master Yoda heads into exile and confusion. Yoda travels on his escape pod to the planet Dagobah but instead lands in the middle of an Imperial fleet. He is spotted by the bridge crew of an Imperial Star Destroyer, who demand his clearance code. Yoda fails to fool them and instead ploughs his escape pod through the Star Destroyer's bridge, sweeping two stormtroopers into space.

The Galactic Empire is hunting down the Jedi including Master Yoda's plucky Padawans. Aboard an Imperial Star Destroyer, an Imperial officer receives a report of Jedi activities on Geonosis. He dispatches an army of former Separatist B1-Series battle droids to the planet to investigate. An MTT transport delivers a detachment of battle droids into the Petranaki arena where they begin inspecting a modified hoverbus.

While sleeping in his meditation chamber, Darth Vader is roused by Emperor Palpatine, who tells him that he owes him Luke Skywalker. Vader informs Palpatine that his spies have told him that bounty hunters are close to finding Skywalker. The Emperor replies "I hope so for your sake."

Now that Darth Vader has recovered the Jedi holocrons, Luke Skywalker and his rebel friends are on the run. Stormtroopers march into the Mos Eisley Cantina. One of them hands the droid-hating Wuher a 1970s still photo of Luke, Princess Leia, Han Solo, and Chewbacca. The bartender denies seeing them.

On Dagobah, Yoda and the Force ghost of Obi-Wan Kenobi contact the former Sith clone Jek-14 by hologram. Jek, who is on Naboo, warns them that Darth Vader has recovered the Jedi holocrons. Kenobi fears about the terrible things that the Emperor can do with them.

After fulfilling his mission to help Luke Skywalker fight the Galactic Empire, Jek-14 prepares to depart Echo Base on Hoth. The Rebel Alliance throws Jek a farewell party. Outside, a wampa is shown riding a tauntaun. Jek tells the rebels that it was a pleasure fighting alongside them but that he must go home. Before departing on his scout fighter, he bids the Heroes of Yavin "May the Force be with you."

Jek-14 has been attacked by Darth Vader while on his way to retirement. Following a brief pursuit, Jek uses his droid arm to destroy the pursuing TIE fighters. He then transforms them into a giant baseball bat and whacks Darth Vader's TIE Advanced fighter away.

An alternate version of "Clash of the Skywalkers".