Thirty years have passed since the Battle of Endor (Return of the Jedi), where both the Emperor and Vader met their doom. During the decades since Endor, the remnants of the Empire have been defeated and the New Republic formed out of the ashes of the Empire. However, enemies against the New Republic still exist. A rogue group of Dark Jedi have emerged that threaten the fragile stability that the New Republic enjoys.
The Cloud City of Bespin has been converted into one of the many Jedi training facilities located all throughout the galaxy. The Jedi's numbers are beginning to grow to Old Republic heights. The New Jedi Order consists of about 7,000 Jedi Knights. Bespin is now the home to both Jedi Masters, Knights and Apprentices.
During routine Jedi training on Bespin, the Dark Jedi invade wearing jet packs, which send them like a swarm dropping into the upper reaches of the cloud city. These Dark Jedi are seeking to re-establish the legacy of Darth Vader and, hence, they wear a more-advanced-looking version of Darth Vader's mask, helmet and body armor in honor of their fallen hero.
As the Dark Jedi attack Bespin, their sleek battle satellites swarm the floating city and rain down turbolaser fire on the city. The Jedi are taken by complete surprise. However, the Dark Jedi seek not to conquer Bespin, but to capture some of the Jedi's prized holocrons, which hold vast quantities of information about the ancient ways and customs of the Jedi. As hundreds of light-saber battles erupt between the Jedi and their Dark Jedi counterparts, some of the Dark Jedi use concussion grenades to cause damage to Bespin's superstructure.
A few of the holocrons are captured by the Dark Jedi. With their mission now complete, the Dark Jedi retreat from Cloud City and fly away from the city using their jet packs which they wear on their backs. The Dark Jedi fly into the nearby clouds and disappear. The roar of engines can be heard as the Dark Jedi escape in their customized Tie Rager star ships, which were hidden in the clouds above Cloud City.
The 12 members of the Jedi Council are present in the Jedi Council chamber in the Jedi Temple on Coruscant. Several Jedi, who survived the battle of Bespin against the Dark Jedi, relate to Luke Skywalker (the head of the Jedi Council) that several Jedi holocrons were taken during the battle. Luke informs the Jedi Council that the Jedi will have to find these lost holocrons and bring the Dark Jedi under control.
Meanwhile, just outside of the Jedi Temple, a shape-shifting Dark Jedi named Asp morphs into Ben Skywalker and enters the Jedi Temple. Asp makes his way to the Jedi super computer area where Asp hopes to disable the Jedi's computer network. Padawans Anakin Solo (son of Han Solo and Leia Organa) and Ben Skywalker (son of Luke Skywalker and Mara Jade) are walking by the computer area. They both sense something and enter the computer area. Ben and Anakin are shocked to see someone in the room that looks exactly like Ben. Asp sees the padawans and flees the room. Ben and Anakin chase after Asp.
Asp makes his way to the garage at the Jedi Temple and steals one of the Jedi swoop bikes. At a high rate of speed, Asp flies down the streets of Coruscant. Ben and Anakin each get a swoop bike and pursue Asp. After a thrilling chase, Asp wrecks his swoop bike. The Coruscant zoo is nearby and Asp enters the zoo to hide from Anakin and Ben. Anakin and Ben park their swoop bikes and quickly follow Asp into the zoo. A spectacular light-saber duel erupts between Asp vs. Ben and Anakin. As the duel rages on, Asp begins to lose so he uses his light saber to release Rygor tigers from their cage.
Ben sees the tigers and says: "I've got a bad feeling about this." The tigers spot Ben and Anakin and then charge at the two padawans. Ben and Anakin battle the tigers. Within in a few minutes, Ben and Anakin have killed all seven of the ferocious tigers. However, by the time Ben and Anakin are finished fighting the tigers, Asp has escaped to parts unknown.
Elsewhere, Shindor, the leader of the Dark Jedi, is elated to learn that some of the Jedi holocrons have successfully been taken from the Jedi. Shindor is currently at the Dark Jedi's cloning facility, which is located on a planet nearby Coruscant. Shindor is using this facility to make clones of Darth Vader and Luke Skywalker. The Dark Jedi plan to fulfill Darth Vader's prophecy that he and Luke should rule the galaxy as father and son and bring peace and order to the galaxy. The Dark Jedi are using Imperial DNA samples of Vader to produce a clone of the Dark Lord of the Sith and are using DNA samples from Luke's severed hand to produce a clone of the venerable Jedi Master. Skywalker's severed hand is currently owned by one of the chief Dark Jedi named, Spiden.
Meanwhile, Spiden hatches a plan to leak the Dark Jedi's efforts to clone Darth Vader and Luke Skywalker to spies working for the New Republic. Spiden hopes the leader of the Dark Jedi will be destroyed by forces from the New Republic so that he can become the new leader of the Dark Jedi. Spiden leaks this information. The New Republic military and a Jedi army plan to raid the Dark Jedi hideout.
Also, Spiden contacts Luke Skywalker and asks the great Jedi Master to meet with him on the planet of Sluivan. Spiden tells Luke that Spiden is a smuggler who came across Lukeís severed hand in a preservation box. Luke learns from Spiden that the Empire recovered Luke's hand that Vader cut off at Bespin. Spiden says that the hand is in perfect condition and can probably be re-attached to Lukeís arm. Luke agrees to meet Spiden on Sluivan.
Luke arrives on Sluivan with R2-D2 and C-3PO. Luke enters a room where Spiden told Luke he would be waiting for Luke. Luke sees Spiden holding his severed hand in a transparent preservation box. Suddenly, the door behind Luke closes. Spiden sets down the hand and pulls out two light sabers. Spiden holds one in each hand and ignites them. Spiden tells Luke that he will now avenge the deaths of Sidious and Vader. Luke pulls out his light saber and ignites it. Luke and Spiden fight with their sabers. Luke manages to cut off one of Spidenís hands. Spiden continues to fight with his other hand. R2-D2 rolls up behind Spiden. R2 ignites his rocket boosters and crashes into the back of Spiden at a tremendous speed. Spiden falls to the ground. Spiden stands back up dazed. With a slight movement of his hand, Luke uses the Force to send Spiden flying across the room. Spiden slams into a wall and is left unconscious. Luke thanks R2 for his valor, then Luke recovers his severed hand and then cuts the closed door open with his light saber . Luke, R2 and C-3PO exit the room. On Coruscant, a team of Jedi doctors re-attach Lukeís hand to his arm.
Luke learns that the Republic is planning to send a military unit to the planet where the Dark Jedi are cloning Vader and Luke. Luke orders the Jedi star pilots to scramble to their fighters and join the Republic forces in the fight. The Republic and Jedi star fighters arrive at the planet where the Dark Jedi cloning facility is located. Hundreds of Dark Jedi fighters are waiting for them. A massive space battle ensues.
Luke and a dozen or so other Jedi make their way to the surface of the planet and enter the Dark Jedi cloning facility. Light saber battles erupt between the Jedi and the Dark Jedi. Luke finds the Dark Jedi leader, Shindor, and they engage in a light-saber duel. Luke eventually decapitates Shindor. The remaining Dark Jedi flee the cloning facility with the growing clones of Vader and Luke. The Jedi set explosive charges all over the cloning facility. The Jedi flee the cloning facility. A few minutes later, the cloning facility is destroyed by the exploding charges.
While the Dark Jedi cloning facility has been destroyed, the New Republic and Jedi are unaware that the Dark Jedi succeeded in preserving the growing clones of Vader and Luke, which will be utilized in the Dark Jedi's grand scheme to conquer the galaxy. Back on Coruscant, Anakin Solo and Ben Skywalker are brought before the Jedi Council. For their bravery in combating the Dark Jedi, the Jedi Council makes Anakin and Ben full-fledged Jedi Knights. The two are given their official Jedi robes. Fade to black. Roll end credits.