After a confrontation between Yoda and a master assassin with a droid army, Yoda must step in to stop another plot to assassinate the king of a strategic planet.
With the starship Malevolence sent after the Jedi fleet, Plo Koon is left stranded with three clone troopers after his fleet gets decimated, trying to fend off more attacks as Anakin and Ahsoka race to rescue them.
With the Republic learning of the new threat of the Malevolence, Anakin rallies the troops along with Ahsoka and Koon to launch a counter-attack on the powerful starship.
When General Grievous captures Padmé Amidala and C-3PO and locks them up on the Malevolence, Anakin and Obi-Wan prepare a rescue mission as they put their final move to destroy the ship into effect.
When droid commandos mount an attack on a distant Jedi outpost, it's up to clone officers Rex and Cody to organize the ranks and raise the spirits of their rookie unit.
When R2-D2 goes missing, Anakin desperately tries to locate him to protect the sensitive information stored in his memory that could give the Separatists the upper hand over the Jedi.
Upon learning of R2-D2's location, Anakin, Ahsoka, and a replacement droid must infiltrate General Grievous's secret post to retrieve R2-D2 and destroy the enemy post.
Padmé's trip to meet with her old friend, Onaconda Farr, on Rodia takes a turn when she learns that he has made a deal with the Separatists, leaving Padmé in a perilous situation.
With the trial of a notorious Separatist leader coming up, Ahsoka and Jedi Master Luminara Unduli have to come up with a plan when Count Dooku sends his assassin to stage a prison break.
When the location of General Grievous's lair is revealed as a punishment for failing Count Dooku, the general squares off against invading Jedi forces to prove his mettle.
Anakin and Obi-Wan's attempt to arrest Count Dooku is interrupted when they discover that he is being held hostage by pirates, who are ransoming him off.
When the pirates double-cross Anakin and Obi-Wan, the latter two find themselves forced to join forces with their mortal enemy, Count Dooku, to break out of their captivity.
When Anakin is injured during a rescue attempt, his life hangs on the line when Ahsoka is forced to bring their ship down on a neutral planet, whose leaders are reluctant to get involved in the current war.
When the Separatists arrive for Anakin, Ahsoka, and the rest, the neutrality of the Lurmen is put to the test when they realize that the Separatists aim to use a powerful weapon against them.
When a clone security force vanishes from a remote outpost, Anakin and Obi-Wan arrive to investigate the desolate planet where the outpost is located, only to get caught in the middle of a conflict between the clones and the native population of the planet.
With the planet of Christophsis besieged by Separatists, Anakin and Obi-Wan lead the charge to free it, only to realize that they have a traitor in their ranks after an ambush.
When Padmé and Jar Jar Binks explore the bio-weapon lab of a nefarious scientist, they end up being taken hostage, leaving Anakin and Obi-Wan to rush to their rescue.
With the release of the virus, those infected have only 48 hours to live. Anakin and Obi-Wan race against the clock to secure the antidote for the stricken, including Padmé and Ahsoka.
With the Separatists taking control of the planet of Ryloth, Anakin and Ahsoka's charge against them takes a turn when the latter disobeys a direct order, leading to some heavy losses.
As Obi-Wan and his forces manage to make it to Ryloth, they are forced to infiltrate a small town that contains a deadly weapon, only to discover that the Separatists are using the town's occupants as shields.
With the Jedi making a push to liberate Ryloth once and for all, they soon discover that they need the help of Twi'lek natives to drive back the Separatists.
When bounty hunters seize the Senate building in an attempt to force the release of Ziro the Hutt, Anakin's presence inside the building throws a wrench in their plans.