| No.overall | No. inseason | Title | Directed by | Written by | Original release date | Prod.code | US viewers(millions) |
| 1 | 1 | "Ambush" | Dave Bullock | Steven Melching | October 3, 2008 (2008-10-03) | 1.08 | 3.99 |
| Jedi Master Yoda must face off against Count Dooku's dreaded assassin Asajj Ventress and her massive droid army to prove the Jedi are strong enough to protect a strategic planet and forge a treaty for the Republic. Ventress fails against Yoda, so Dooku tells Ventress to kill the king of the planet, who wants to sign the treaty with the Republic. Yoda protects the king from Ventress, who then flees. |
| 2 | 2 | "Rising Malevolence" | Dave Filoni | Steven Melching | October 3, 2008 (2008-10-03) | 1.07 | 3.92 |
| An attack by a devastating new Separatist weapon—the powerful starship Malevolence—leaves Jedi Master Plo Koon and his clone troopers struggling to survive until Anakin and Ahsoka can find them. |
| 3 | 3 | "Shadow of Malevolence" | Brian Kalin O'Connell | Steven Melching | October 10, 2008 (2008-10-10) | 1.09 | 2.8 |
| With the help of his Padawan, Ahsoka, and Jedi Master Plo Koon, Anakin uses new long-range Y-wing bombers to lead a bold strike on General Grievous's warship, the Malevolence, and its destructive weapon. |
| 4 | 4 | "Destroy Malevolence" | Brian Kalin O'Connell | Steven Melching | October 17, 2008 (2008-10-17) | 1.11 | N/A |
| Padmé Amidala and C-3PO are taken hostage by General Grievous, leaving Anakin and Obi-Wan to save the senator and complete the destruction of the Malevolence. |
| 5 | 5 | "Rookies" | Justin Ridge | Steven Melching | October 24, 2008 (2008-10-24) | 1.14 | N/A |
| Alone on a distant outpost, clone officers Rex and Cody must inspire their rookie unit to believe in themselves to stave off a droid commando invasion. |
| 6 | 6 | "Downfall of a Droid" | Rob Coleman | George Krstic | November 7, 2008 (2008-11-07) | 1.02 | N/A |
| R2-D2 is lost during a fierce space battle—and Anakin must find him before the Separatists discover the Jedi military secrets locked in his memory banks. |
| 7 | 7 | "Duel of the Droids" | Rob Coleman | Kevin Campbell & Henry Gilroy | November 14, 2008 (2008-11-14) | 1.06 | N/A |
| Anakin, Ahsoka, and replacement droid R3-S6 embark on a dual rescue/sabotage mission when they discover that R2-D2 is being held at General Grievous's secret enemy listening post, Skytop Station. |
| 8 | 8 | "Bombad Jedi" | Jesse Yeh | Kevin Rubio & Steven Melching & Henry Gilroy | November 21, 2008 (2008-11-21) | 1.05 | 2.77 |
| On a diplomatic mission to the planet Rodia, Padmé discovers that her old friend and fellow Republic senator Onaconda Farr has allied his planet with the Separatists. In exchange for food and resources for his people, Onaconda captures Padmé and promises to deliver her to Nute Gunray. Sensing that Padmé is in trouble, Jar Jar Binks disguises himself as a Jedi and, with the help of C-3PO, courageously fights to rescue his friend and fellow senator. |
| 9 | 9 | "Cloak of Darkness" | Dave Filoni | Paul Dini | December 5, 2008 (2008-12-05) | 1.10 | 1.95 |
| Ahsoka and Jedi Master Luminara Unduli escort the captured notorious Separatist leader Nute Gunray to Coruscant so he can stand trial for his crimes. However, they are unaware that Count Dooku has sent his assassin, Asajj Ventress, to free their captive. With the help of Senate Commandos, the Jedi have to thwart Ventress's efforts to free their prisoner, despite the traitorous plans of Senate Guard Captain Argyus. |
| 10 | 10 | "Lair of Grievous" | Atsushi Takeuchi | Henry Gilroy | December 12, 2008 (2008-12-12) | 1.12 | 2.14 |
| Jedi Master Kit Fisto and his former Padawan, the Mon Calamari Jedi Nahdar Vebb, track escaped prisoner Nute Gunray to a remote world. Following Nute into a mysterious den filled with strange creatures, weapons, and war-time artifacts, the Jedi discover that it is the trap-laden lair of General Grievous. Learning that Count Dooku has led the Jedi there in order to punish Grievous for his recent failures, the general is determined to prove his abilities and destroy the Jedi. Kit and Nahdar, along with a contingent of clones, must now fight their way past Grievous and his caretaker droid A-4D to avoid being caught in Grievous's evil clutches forever. |
| 11 | 11 | "Dooku Captured" | Jesse Yeh | Julie Siege | January 2, 2009 (2009-01-02) | 1.16 | N/A |
| During their own attempt to kidnap Dooku, Anakin and Obi-Wan discover that the Sith lord has already been captured by pirates. Hondo Ohnaka and his gang of pirates hold Dooku captive in their den on Florrum, and hold him for ransom. It is up to Anakin and Obi-Wan to see if the offer is too good to be true. |
| 12 | 12 | "The Gungan General" | Justin Ridge | Julie Siege | January 9, 2009 (2009-01-09) | 1.20 | 2.31 |
| Anakin and Obi-Wan have been duped and are being held for ransom, along with Count Dooku, by the pirate chief Hondo Ohnaka and his second-in-command, Turk Falso. While Anakin, Obi-Wan, and Dooku unsuccessfully attempt to escape, the Republic sends the ransom via a special envoy, including Representative Jar Jar Binks. When Falso tries to steal the ransom from his boss by shooting down the shuttle, the only survivors are a squad of clones and Jar Jar, who, as the most senior officer alive, has to take charge of the mission. It becomes a race against time as Jar Jar rushes to deliver the ransom to take custody of Dooku and save the Jedi. |
| 13 | 13 | "Jedi Crash" | Rob Coleman | Katie Lucas | January 16, 2009 (2009-01-16) | 1.22 | 2.35 |
| Anakin and Ahsoka arrive at a pitched sky battle to help besieged Jedi General Aayla Secura. Anakin is gravely injured in the fight. Aayla and Ahsoka, along with the now-wounded Anakin, Rex, and the surviving clones, crash land on the uncharted grass-covered planet Maridun. Forced to leave Anakin behind in order to save him, Aayla teaches Ahsoka why the Jedi have no personal attachments. They make their way to a Lurmen village. Their ruler, Tee Watt Kaa, explains that they are pacifists in this war and not aligned with either side. Hesitant to have anything to do with the Jedi, Kaa agrees to help save Anakin's life. |
| 14 | 14 | "Defenders of Peace" | Steward Lee | Bill Canterbury | January 23, 2009 (2009-01-23) | 1.24 | 2.17 |
| Tee Watt Kaa refuses to shelter the Jedi from arriving Separatist forces, fearing that such an action would unnecessarily bring his neutral people into the war. Ahsoka, Aayla, the wounded Anakin, and the rest of the clones respect their wishes as they do not want to jeopardize the village with their presence, so they have to retreat into the wilds of the planet. Separatist Neimoidian General Lok Durd arrives to test a devastating weapon, which they plan to use on the Lurmen. Ultimately, the villagers have to decide whether they will surrender to the Separatists or fight with the Jedi to defend their village. |
| 15 | 15 | "Trespass" | Brian Kalin O'Connell | Steven Melching | January 30, 2009 (2009-01-30) | 1.25 | 2.62 |
| Arriving on the desolate ice world of Orto Plutonia, Anakin and Obi-Wan investigate the disappearance of a clone security force stationed on a remote outpost. The Jedi, accompanied by Senator Riyo Chuchi and Chairman Cho of the nearby moon of Pantora, soon discover their clone troopers were attacked by a tribe of furry natives known as the Talz. Fierce beast-riding warriors, the Talz are very territorial and only want to be left alone. The Jedi manage to negotiate peace with the Talz chieftain, Thi-Sen, when greedy Chairman Cho breaks it by insisting that the planet and the Talz are under his power. The resulting conflict escalates into war between the clones and the Talz, with the Jedi caught in the middle. |
| 16 | 16 | "The Hidden Enemy" | Steward Lee | Drew Z. Greenberg | February 6, 2009 (2009-02-06) | 2.01 | 2.51 |
| Anakin and Obi-Wan lead Republic forces in an attempt to defeat the droid armies and free the planet of Christophsis from the Separatist siege. When the Republic is ambushed and forced to retreat, it becomes clear that someone in their midst has set them up. The Jedi believe this infiltration is a Sith-backed operation and go behind enemy lines to investigate. Meanwhile, Captain Rex and Commander Cody set out to uncover the traitor amongst them. Dave Filoni, the supervising director of the series, refers to the betrayal of the Republic by a clone trooper as them having "gone Jango", saying that "they have a little too much of Jango Fett in them". The episode went through numerous changes during production. Slick was originally planned to have red hair in the episode. However, when rendered, the dark hair model that was standard for clone troopers was used instead, helping him blend in with the rest of the clones rather than stick out as a potential suspect. The script of the episode had the opening sequence feature the clone troopers preparing a combat droid known as "The Beast", which resembled the dome-shaped mining droids from the original Star Wars film and a head of the Dalek from the British program Doctor Who. The sequence was cut from the episode, as it was decided to keep the 2 opposing sides fixed as "clones versus droids", and the scene involving "The Beast", whose function was not revealed, unnecessarily complicated the storyline. Most of the main voice actors in the series appeared in the episode. The episode's opening was narrated by Tom Kane, while Matt Lanter voices Anakin Skywalker and James Arnold Taylor voices Obi-Wan Kenobi and the tactical droid. Nika Futterman returns as Asajj Ventress in the episode. Dee Bradley Baker voices the clone troopers in the episode, including Captain Rex and Commander Cody. Matthew Wood provided the voices of the battle droids. "The Hidden Enemy" takes place on Christophsis, the first episode in the series to do so. The planet was previously featured in the 2008 Star Wars: The Clone Wars film. The episode is placed second chronologically in the series, after season 2, episode 16, "Cat and Mouse", and before the Star Wars: The Clone Wars film. The episode was meant to serve as a prequel to the film. Eric Goldman from IGN called it "another solid episode", praising its opening battle sequence, Obi-Wan Kenobi's dialogue with Asajj Ventress, and Captain Rex and Commander Cody's strategy to catch Slick, although he did note that Ventress' appearance in the episode felt "a bit unnecessary". He ultimately gave the episode a "great" rating of 8.5 out of 10. Dan Zehr from Coffee With Kenobi commended the episode, calling the chase sequence involving Rex, Cody, and Slick "thrilling" and saying that the episode was "integral to disseminating the mystery that will eventually become Order 66". Zehr praised the anthology structure of the series, calling it "quite brilliant", and said he was even more impressed with Dave Filoni after watching the episode. Susan Lulgjuraj from FanSided said that the episode makes the clone troopers feel like individuals, thus revealing their "dark side", and it raises moral questions about the clones' rights and freedoms. |
| 17 | 17 | "Blue Shadow Virus" | Giancarlo Volpe | Craig Titley | February 13, 2009 (2009-02-13) | 1.26 | 2.94 |
| The Republic discovers a Separatist bio-weapon lab hidden on the planet of Naboo. Rather than wait for help, Padmé explores the lab with Jar Jar. Anakin, Ahsoka, Rex, and Obi-Wan arrive and follow after her. They find that the Senator is being held captive by the sinister Dr. Nuvo Vindi. The mad scientist has been developing a lethal virus for the Separatists. Vindi threatens to set off a bomb and release the virus. |
| 18 | 18 | "Mystery of a Thousand Moons" | Jesse Yeh | Brian Larsen | February 13, 2009 (2009-02-13) | 2.02 | 2.11 |
| Even though the lab has been shut down, Dr. Vindi manages to activate the dreaded Blue Shadow Virus, infecting Ahsoka, Padmé, and many clone troopers. The plague is fatal within 48 hours. Anakin and Obi-Wan must travel to the mysterious planet Iego to secure the only known antidote to the sickness. They arrive to find its population living in fear of a mysterious force that has been killing anything that tries to leave their world. With the help of Jaybo Hood, a clever Iegoan boy, Anakin and Obi-Wan must solve the planet's mystery before they can leave, and before everyone infected with the Separatist virus dies. |
| 19 | 19 | "Storm Over Ryloth" | Brian Kalin O'Connell | George Krstic & Scott Murphy & Henry Gilroy | February 27, 2009 (2009-02-27) | 1.15 | 2.37 |
| Ryloth, home world of the Twi'lek people, has been subjected to military occupation by the droid army of the Separatists and surrounded by a blockade of Trade Federation battleships. While launching a surprise attack against the blockade, Ahsoka disobeys Anakin's orders and ends up losing most of her squadron. Even though she is emotionally rocked by this failure, Anakin helps her learn to persevere, placing her in charge of another risky attack. |
| 20 | 20 | "Innocents of Ryloth" | Justin Ridge | Randy Stradley & Henry Gilroy | March 6, 2009 (2009-03-06) | 1.17 | 2.49 |
| With the space blockade around Ryloth destroyed, Obi-Wan must lead a small clone force into a droid-occupied town to sabotage their anti-aircraft guns. Obi-Wan's mission is complicated when he learns the town's inhabitants are being used as living shields. A pair of clones in his platoon forges an unlikely friendship with a refugee Twi'lek girl, Numa, who has been orphaned by the war. Through their relationship with her, the clones begin to understand the real cost of the war. |
| 21 | 21 | "Liberty on Ryloth" | Rob Coleman | Henry Gilroy | March 13, 2009 (2009-03-13) | 1.19 | 3.01 |
| The battle for Ryloth rages as the Republic attempts to drive off the occupying droid army led by Techno Union foreman Wat Tambor. With his forces stretched thin, Mace Windu must convince Twi'lek freedom fighter Cham Syndulla to help him save the capital city from the droids' destruction. Initially, the Twi'lek hero is hesitant to aid Mace, but ultimately he realizes that the Jedi can be trusted and joins with him to liberate the city—and ultimately the planet—in the climactic battle. |
| 22 | 22 | "Hostage Crisis" | Giancarlo Volpe | Eoghan Mahony | March 20, 2009 (2009-03-20) | 2.04 | 3.29 |
| In an attempt to force the release of the crime lord Ziro the Hutt from prison, bounty hunters seize control of the Senate Building and hold members of the Senate hostage. Cad Bane, the leader of the operation, with the help of bounty hunter Aurra Sing, issues his demands to Chancellor Palpatine, who has no choice but to meet his request. Unbeknownst to the hunters, Anakin is loose in the Senate building. Hostage Crisis received attention for it being the episode that contained the debut of Cad Bane. The episode was generally well received for its willingness to portray violence, but drew criticism for its inclusion of Ziro the Hutt, due to that character being seen as uninteresting and as an offensive LGBT stereotype. The effectiveness of the episode's portrayal of Anakin Skywalker was disputed among critics. |
