While having a pre-graduation test in Kamino, Domino squad fail to work as a team and are forced to work side by side, otherwise they will be dropped out. On the other hand, Shaak Ti, Bric and El-Les argue about the clone cadets' future, believing that it will fall through.
Anakin and Obi-Wan head to Kamino to warn Shaak Ti and Lama Su off the Separatists, who are launching a space battle against the Republic in association with General Grievous, leading to the death of soldier 99. Fives and Echo manage to deal with the attack and are promoted as ARC troopers.
As the Separatists launch another blockade attack on Ryloth, Jedi Master Di asks Dao to provide them with help, but he himself is under attack, leaving no way for the Jedi Council except reaching out for Senator Organa to ask King Katuunko to make use of his planet to help Ryloth survive.
When the daughters' of the Chairman Papanoida are abducted on board a Trade Federation battleship, Ahsoka and Senator Chuchi help Papanoida find the captor's place and monitor him, only to discover that officer Sib Canay, the Separatist traitor, is behind everything, and save the girls.
In the Mandalorians' capital city, Sundari, Padmé makes a visit to Duchess Satine's palace for diplomatic matters. Meanwhile, a gang of Moogans smuggle tea with a toxic chemical and distribute it on schools; as a result, a lot of children is hospitalized, and Padmé investigates the situation.
On Mandalore, Ahsoka is sent on a teaching mission, to uncover a plot masterminded by Prime Minister Almec, who turns out to be affiliated to the Mandalorian black market. Ahsoka and the clone cadets manage to defeat Almec before he goes as planned with his scheme.
During a political mission, Ahsoka is appointed to protect Senator Padmé by the Jedi Council, but she starts seeing visions of the Senator being assassinated by the fugitive, Aurra Sing. Ahsoka's visions come true when Aurra attempts to kill the Senator, and she manages to hunt down the fugitive.
While doing shopping, C-3PO is kidnapped by the fugitive, Cad Bane, who wants to get access to his brain to get some data regarding the Senate. But when he finds no useful information in C-3PO, he abducts R2-D2 and obtains the information he needed.
After he is under lock and key, Ziro the Hutt breaks out from prison, and Cad Bane is assigned to arrest him to find out about the data that he has obtained about the Senate. As Obi-Wan Kenobi and Quinlan Vos are also searching for him, the bounty hunter, Snooty, is finally able to kill Ziro.
As Padmé and Ahsoka decide to visit their friend, Senator Bonteri, who is affiliated to the Separatists, they disguise themselves to enter Raxus. After they are able to build bridges between the Republic and Separatists, Dooku does the last thing they expected to happen.
As the Republic's Senators collect funds to buy five million new clone troops, Senators Padmé, Organa and Onaconda stand in the way of the new bill and are as well ambushed by fugitives.
Darth Sidiois realizes that Asajj Ventress is taking advantage of the dark side of the Force which is making her grow more power, so he summons Count Dooku to assassinate her. But when she survives the attempted murder, Dooku seeks revenge on her, putting her Nightsisters in his retaliation scheme.
The Nightsisters reach out for Count Dooku to overthrow Ventress. Talzin and Asajj hand-pick a warrior called Savage Opress, train him, and transform him into a hulking warrior, after which they send him to Dooku, whom he will help to haunt down Ventress and Darth Sidious.
Anakin and Obi-Wan are on a mission to find out about Savage Opress, who has been trained in the ways of the Sith by Count Dooku. Opress clashes with the Jedi and kills King Katuunko. Ventress flees and Dooku takes the battle to his side and wins out.
In an attempt to find out whether Anakin is the Chosen one, the dark Force leads Anakin, Obi-Wan, and Ahsoka to a distant planet. Three powers known as the Father, Daughter, and Son show up when the Father tries to convince Anakin to take his place when it turns out that he is the Chosen one.
The Son abducts Ahsoka and threatens him in order to combine their forces to overpower the forces of his Father and Sister. Moreover, the Son casts a Sith spell against Ahsoka, leading into a battle between the patriarch family that ended with the Daughter sacrificing herself for her Father.
With the Jedi stuck in Mortis, the Son pressures on Anakin to take advantage of his force. The spell the Son cast starts driving Anakin into a series of hallucinations about his dark future, and the Son convinces him that this could be ended if only he approves to combine their forces.
An elite team of Jedi and clone troopers led by Obi-Wan and Anakin, along with R2-D2 and a squad of droids, are assigned to rescue Jedi General, Even Piell, from the fugitives who hold him captive in an impassable prison.
After breaking into the Citadel, Obi-Wan and Anakin try to find a way to make their headway, but they're faced with many obstacles they didn't expect. After they're ambushed and threatened by weapons, ARC trooper Echo dies, and the team flees to the caves, calling the Jedi Temple to help them out.
After they are out of the citadel and their ship is destroyed, Anakin and Obi-Wan are forced to wait for the Republic fleet to save them, but they are attacked by a band of droid squads. The Jedi Council sends Plo Koon who arrives and rescues the Jedi, taking them back to Coruscant.
A battle begins on Felucia and Ahsoka is abducted by Trandoshans, and she finds herself with other Jedi Masters, whom she plans with to make their headway. But when they attempt to escape the next day, the Trandoshans spot them and lock them up.
After Ahsoka and the Jedi younglings fail to escape the Trandoshans, they realize that they have abducted a new Wookie called Chewie, whom they manage to set free. Ahsoka and Chewie attack the Trandoshan and kill a large number of them, after which Ahsoka finally kills the Trandoshan's gangster.