A long awaited truth! A distress signal has been received at the Jedi Temple and Master Plo Koon has been dispatched to investigate its origin. The signal is from a ship thought to be lost and was last known to be in the possession of a Jedi Master who was killed long ago....

The clone troopers of the 104th Battalion -- the Wolf Pack -- work their way through a choking sandstorm that obscures visibility on the windswept surface of a desert moon orbiting Oba Diah. A sandblasted Jedi shuttle is spotted. Wolffe confirms the shuttle's serial number -- T-6 shuttle number 775519 and Plo Koon finds a functional, if sandlogged, blue-bladed lightsaber in the wreckage. He orders his troops to clear the entire area and ready the entire wreck for transport back to Coruscant.

Plo Koon contacts the Jedi Council and confirms that the shuttle and lightsaber belong to the long-lost Jedi Master, Sifo-Dyas. Obi-Wan Kenobi recounts the history of Sifo-Dyas. He was a leading member of the Jedi Council prior to the blockade on Naboo, until the rest of the Council judged his ideas to be too extreme. Sifo-Dyas foresaw a coming conflict and was convinced the Republic needed to raise an army. The Council rejected these ideas, and evidently Sifo-Dyas somehow secretly commissioned the Kaminoans to create the clone army.

The analysis of this newfound information continues in the Jedi war room, where Madame Jocasta Nu prepares a briefing on the mysterious circumstances surrounding Master Sifo-Dyas' death. Jedi records indicate he died on Felucia, during a failed attempt to quell a skirmish among local tribes. There is no record of the whereabouts of his body, however, as the entire incident has been sealed and classified by the office of the Supreme Chancellor. Yoda assigns Anakin and Obi-Wan to investigate.

Yoda visits Supreme Chancellor Palpatine in his executive offices to discuss the sealed records. Palpatine has no recollection of Sifo-Dyas' name, but when Yoda describes his disappearance over a decade ago, the Chancellor explains he was but a humble senator from Naboo at the time. Palpatine recommends that Yoda speak with his predecessor, former Chancellor Valorum.

As Yoda departs Palpatine's office, he receives a holographic update from Kenobi and Skywalker. Obi-Wan explains that, though the primitive Felucians were difficult to understand, they confirmed that Sifo-Dyas was not alone when he visited the planet. He was in the company of a second Jedi, whose identity cannot be confirmed. The trail of Sifo-Dyas goes cold when Kenobi confirms that the Jedi Master's body was cremated by the Felucians.

Speaking with Valorum at the former Chancellor's residence, Yoda learns that Valorum had assigned Sifo-Dyas on a secret mission to deal with the Pyke syndicate -- a powerful part of the spice cartel. Sifo-Dyas was never able to complete this mission, as he was called by the Jedi Council to deal with the conflict on Felucia. But who was the second Jedi the Felucians spoke of? Valorum knows of no second Jedi, but offers that his personal aide, Silman, accompanied Sifo-Dyas on the mission to deal with the Pykes, and was also diverted to Felucia.

At Count Dooku's estate on Serenno, the towering holographic form of Darth Sidious contacts his apprentice, Darth Tyranus. Sidious seems furious, demanding to know why the Jedi are sniffing around the loose end that is Sifo-Dyas. He commands Tyranus to clean up his affairs lest their plans be threatened. Sidious makes sure Tyranus understands the price of failure by briefly telekinetically choking his apprentice with the Force.

Back at the Jedi Temple war room, Obi-Wan Kenobi continues his updates from Felucia. The Felucians have no recollection of Silman. A look through Republic records provides a single holographic image of Silman wearing a medallion with the symbol of Valorum's office. Obi-Wan is exasperated by how compounded the mystery has become.

The only tenuous lead the Jedi have is Chancellor Valorum's report that he sent Sifo-Dyas and Silman to Oba Diah. Yoda orders Skywalker and Kenobi to visit the Pykes on Oba Diah. Skywalker and Kenobi land their shuttle at the base of the massive obsidian fortress from where Lom rules the Pyke Syndicate.

The Jedi walk their way past spice-addled dregs to Lom's throne, where he greets them with an insincere grin. When Obi-Wan mentions Sifo-Dyas' name, there is a flicker of recognition in Lom's glassy eyes, but he explains that was so long ago. He knows nothing of the recent discovery of Sifo-Dyas' ship.

Around Lom's neck, Obi-Wan spots the medallion that Silman wore in the holograph. Lom tries to draw attention away from the crest, but Anakin loses his patience and jerks the necklace clear off Lom's neck with the Force. Chuckling, Lom eventually concedes that the man the Jedi are looking for is here on Oba Diah.

In the depths of the Pyke dungeons, Lom leads Obi-Wan and Anakin to a cell, explaining the Pykes' involvement in the mystery of Sifo-Dyas. Over a decade ago, the Pykes wished to gain an advantage over rival crime families, so they struck a deal with a powerful man named Tyranus. This man hired the Pyke syndicate to kill Jedi Master Sifo-Dyas. The Pykes complied by shooting down Sifo-Dyas' shuttle over the Oba Diah moon. They inspected the wreckage, and turned over Sifo-Dyas' body to Tyranus as proof of their deal fulfilled.

However, the Pykes also discovered Silman aboard, who had survived the crash. Recognizing that dealing with someone as mysterious and unpredictable as Tyranus would require a degree of insurance, the Pykes kept Silman a secret, and locked him up. Now, over a decade later, Lom cashes in this insurance, asking Obi-Wan and Anakin to forgive the murder of Sifo-Dyas in exchange for the return of Silman. Kenobi and Skywalker enter the darkened cell from which emerges a wretched, bedraggled and starving man.

The unkempt prisoner is Silman, who has gone mad in the years since his captivity. Meanwhile, Count Dooku arrives at the Pyke stronghold, landing his solar sailer on the landing platform and Force-hurling the Pyke guards that try to block his path.

Kenobi tries to question Silman, but the deranged prisoner seems more focused on feeding the vermin and lice that crawl over his body. In his peculiar way, Silman explains that the Pykes had betrayed Sifo-Dyas, but they were not the ones ultimately responsible for his fate. Someone else, more powerful wanted Sifo-Dyas dead so that he could steal his identity. But before Silman can say any more, he is strangled to death by the dark side of the Force. Count Dooku has tied up this loose end.

Anakin and Obi-Wan turn to confront Dooku, who ignites his lightsaber. The Jedi light their blades and engage Dooku in a duel. In his classical fighting style, Dooku defends himself, bringing the duel to the open landing platform. Lom emerges from the stronghold flanked by Pyke guards. He says to Dooku their business is over, and calls him by the name Tyranus, revealing this identity to the Jedi.

Dooku Force-pushes his way past the guards and slays Lom. Dooku leaps off the landing platform onto a passing cargo freighter. He calls for his pilot droid to pick him up. Anakin leaps onto the freighter (propelled by a Force-throw from Obi-Wan) in a last, desperate attempt to stop Dooku.

The count sacrifices the freighter by slicing one of its engines, causing the entire ship to drop. Dooku jumps to safety on his waiting solar sailer and escapes.

The Jedi Council discusses these alarming new discoveries. It is clear that the Sith were involved in the creation of the clone army, but with the Jedi Order so enmeshed in the war, they have no option but to continue. Yoda and the Jedi believe in the clones, having fought alongside on them on so many fronts. But it is evident that whatever the Sith master plan is, it is coming to fruition. With regret, Yoda voices the conclusion that the Jedi have no choice but to carry on, playing the unseen Sith Lord's game.