After a signal is detected coming from a moon of the planet Oba Diah, Plo Koon and his clone troopers are sent to investigate. Amid a howling sandstorm, they find the wreck of a crashed shuttle, with a lightsaber on board. The lightsaber belongs to long-dead Jedi Master Sifo-Dyas, the one who ordered the creation of the clone army, who apparently died on Felucia while attempting to negotiate peace between two warring tribes. Master Plo orders the wreck be taken back to Coruscant.
The Jedi are understandably intrigued. Obi-Wan, reporting from Felucia, says that the tribal leaders, from what he could understand, told him that Sifo-Dyas was accompanied by another Jedi, and they cremated his body. It's also discovered that Sifo-Dyas' records have been sealed by the office of the Supreme Chancellor. Yoda goes to talk to Palpatine, who says that this happened before his time in office and so he doesn't know why the records would have been sealed. He suggests Yoda speak to his predecessor, Finis Valorum.
Valorum tells Yoda that he sent Sifo-Dyas to negotiate with the Pyke Syndicate to avoid a full-scale war in the galactic underworld. But the negotiations never took place, he says, because the Jedi Council ordered Sifo-Dyas to Felucia to settle a tribal dispute. Yoda asks him which other Jedi he sent with Sifo-Dyas. Valorum is surprised, because he didn't send another Jedi he sent his personal aide, a man named Silman.
Anakin and Obi-Wan are sent to Oba Diah to talk to the Pykes. While talking with Minister Lom Pyke, he says he remembers Sifo-Dyas' visit, but can't give them any more information. However, after the Jedi notice that Lom is wearing the necklace with Valorum's symbol of office on it that belonged to Silman, he spills: the Pykes were hired by a man called Tyranus to kill Sifo-Dyas, so they shot down his ship. They found Silman still alive at the crash site, and have been holding him in their dungeon as leverage ever since. Obi-Wan recognizes the name, recalling when Jango Fett told him that he had been recruited by a man named Tyranus to be the Clone Army template.
Count Dooku knows that Darth Sidious is angry with him, because he didn't do enough to tidy up the loose ends regarding Sifo-Dyas. Sidious Force-chokes him from across the galaxy to make his point. So Dooku, known to the Pykes as Tyranus, arrives on Oba Diah to deal with those loose ends.
Anakin and Obi-Wan find that Silman has gone mad from the isolation, and no longer wants to leave his cell. But he does manage to give them some information that the man who hired the Pykes wanted Sifo-Dyas dead because he wanted to be Sifo-Dyas. Obi-Wan is trying to get Silman to elaborate on who that was when the question is answered for them, when Count Dooku makes his presence known by Force-choking Silman to death.
A fight ensues, taking the Jedi and Sith from the cells to an outside platform. There, Minister Lom and his guards arrive, and Lom tells Dooku he's not welcome.
Obi-Wan: Tyranus? You are the man called Tyranus?
Dooku kills Lom, and shortly escapes in his ship. Anakin and Obi-Wan report back to the Jedi Council on what they've discovered. Yoda decides that they will say nothing, not even to the Chancellor, about the Sith being behind the creation of the clone army. At the moment, the Jedi have no choice but to play the Sith Lord's game.
- As You Know: The Jedi Council discuss the events surrounding Sifo-Dyas, including the discovery that he created the clone army prior to his death, even though Obi-Wan had previously told Yoda everything in Attack of the Clones.
- But Thou Must!: Even though the Jedi now know that the Sith had a hand in the creation of the clone army, they have no choice but to keep using them, as the clones are the only thing standing between the Republic and the Separatist droid army.
- The Phantom Menace wasn't the first time Chancellor Valorum sent Jedi on a secret mission.
- This episode follows up on the mentions of Sifo-Dyas in Attack of the Clones; we finally learn exactly what happened to him.
- At the Council meeting at the end, when Mace Windu says that they had, in the past, judged Sifo-Dyas' views on the creation of an army too harshly, Obi-Wan responds, "Well, it's not the first time we've been wrong recently, is it?" a clear allusion to the decision to bow to the Senate's wishes and expel Ahsoka from the Order when she was framed for treason in "The Wrong Jedi". Obi-Wan was one of three Council members to vote against it.
- Call-Forward: When Yoda declares that the Council will conceal the fact that the Sith were behind the creation of the clone army, Anakin looks distinctly unhappy.
- Chekhov's Gun: Anakin, looking at Silman's picture, takes note of the necklace he's wearing. Then, it turns up around the neck of Minister Lom...
- Clones Are People, Too: Yoda, when deciding that the Jedi Council will conceal the role of the Sith in the creation of the clone army, notes that the clone troopers have proven to be valiant men and it's unspoken but clear that they are in no way to blame for this.
- Dead Person Impersonation: Why Dooku had Sifo-Dyas killed so that he could take control over the clone army's production from him.
- Fastball Special: Obi-Wan uses the Force to throw Anakin after Dooku when the latter has jumped onto a passing ship.
- Sidious Force-chokes Dooku from across the galaxy: Sidious is on Coruscant, and Dooku is on Serenno.
- Dooku kills Silman as well as his guards by choking them with the Force.
- Freeze-Frame Bonus: When Dooku arrives on Oba Diah, a ship the same model as the Twilight can briefly be seen flying above.
- Genre Shift: This episode returns to the Noir-esque vibes that Obi-Wan's storyline in Attack Of The Clones featured. Fitting, given that this episode retreads over a good chunk of that plotline's unresolved questions.
- Go Mad from the Isolation: Silman has been locked up alone in a cell for over a decade. It's amazing he could still give the Jedi the information about why Sifo-Dyas was killed, since he now considers the maggots in his cell his "friends".
- He Knows Too Much: The reason why Dooku kills Silman and Lom, and also likely part of the reason for Sifo-Dyas' death as well.
- Impaled with Extreme Prejudice: Dooku kills Lom this way.
- Internal Reveal: The Jedi finally find out that Dooku is Tyranus.
- Lampshade Hanging: Dooku taunts Obi-Wan that he outight told him all the important parts on Geonosis before the war and the Jedi really should have put the pieces together immediately.
- Posthumous Character: Sifo-Dyas is long dead, but his influence as a former member of the Jedi Council is still being felt. He made a convenient scapegoat to pin the clone army on because he had foreseen the Clone Wars coming in visions and advocated for an army to be ready for the conflict. Judging by his hologram, he was also a man of regal bearing and a natty dresser, with fine, high-collared Jedi robes.
- The Reveal: We, and the Jedi, finally learn the truth about Sifo-Dyas' role in the creation of the clones and his demise: Sifo-Dyas was indeed the one who placed the order for the clone army, partially due to Dooku's suggestion. Dooku, using his Sith name "Tyranus", then hired the Pykes to assassinate Sifo-Dyas by shooting down his shuttle, allowing Dooku, and by extension Sidious, to take control over the production of the clones by claiming to be Sifo-Dyas' representatives, up to and including picking Jango Fett to be the army's template.
- Revealing Cover-Up: Anakin and Obi-Wan are having a hard time getting Silman, who has gone mad after a decade in the Pykes' dungeon, to coherently explain who had Sifo-Dyas killed, when Dooku, sent to Oba Diah by Sidious to clean up this loose end, announces his presence by Force-choking Silman giving the Jedi the answer they were looking for.
- Signature Item Clue:
- Sifo-Dyas' lightsaber is found on the crashed shuttle on Oba Diah's moon, which is a dead giveaway he didn't die on Felucia.
- Anakin and Obi-Wan catch Lom in a lie because they notice he's wearing Silman's necklace.
- Spanner in the Works: Lom, both by keeping Silman alive so the Jedi could get some information out of him, and for essentially giving the Jedi Dooku's Sith title.
- You Have Failed Me: Sidious makes it clear to Dooku what fate awaits him if he fails to cover up Sifo-Dyas' trail.