The Jedi's presence on Mon Calamari cannot stop the Mon Calamar and the Quarren from falling into civil war after the death of their ruler, thanks to the arrival of the Separatist Riff Tamson. While Anakin, Padme, Kit Fisto, and Ahsoka try to repel a droid invasion, Captain Ackbar hopes to teach the young Mon Calamari prince to step up and lead his people.
As a new front in the Clone Wars opens in the waters of Mon Calamari, the Jedi Council appeals to the Gungans for reinforcements. When the Separatists gain the upper hand, Ahsoka is tasked with keeping Prince Lee-Char alive and out of enemy hands.
In Mon Calamar's darkest hour, Lee-Char and Ahsoka attempt to rally both the Mon Calamari and the Quarren to turn back the Separatist forces and take back control of their world. Meanwhile, Riff Tamson tortures his Jedi prisoners Anakin Skywalker and Kit Fisto.
When it becomes clear that the Gungan leader Boss Lyonie is being manipulated by a close adviser to turn against the Naboo, Jar Jar must take advantage of his resemblance to the leader to prevent the start of a war.
C-3PO and R2-D2 join Commander Wolffe on a relief mission to the planet Aleen, which has been rocked by deadly earthquakes, where the droids find themselves in the middle of a hidden conflict with creatures that live beneath the planet's surface.
While returning home C-3P0 and R2-D2 crash-land on a primitive world, where they must negotiate with a head-strong leader in order to continue on their journey.
The clones follow Skywalker into the theater of battle to take control of the capital of Umbara, but struggle after the headstrong General Pong Krell takes command of their mission.
When the tide of battle on Umbara turns against the Republic forces, Krell leads Rex and his squadron to take a strategic airbase. But the clones worry that the General's strategy against the enemy's advanced technology will get them all killed.
After General Krell orders the clones to advance on the heavily fortified Umbaran capital, Fives, Jesse, and Hardcase disobey orders to execute a covert plan of their own.
When Pong Krell threatens to execute two of the clones for disobeying orders, Captain Rex is forced to confront his own commander -- forcing the Jedi to show his true colors.
Anakin and Ahsoka investigate the disappearance of a colony of Togrutans and discover that the Zygerrians, in league with the Separatists, are hoping to rebuild their slavers empire.
The Jedi plan to rescue the colonists is complicated when Rex and Obi-Wan are captured and sent to the slave camps of Kadavo. Anakin confronts the Zygerrian Queen as Count Dooku arrives to take control of the situation.
Lux Bonteri interrupts a peace summit on Mandalore to renounce the Separatists, blaming Dooku for the murder of his mother -- and dragging Ahsoka into a deadly meeting with the extremist faction called the Death Watch.
Obi-Wan fakes his death at the hands of the criminal Rako Hardeen in order to assume the man's identity, going undercover inside a Republic prison to get to the bottom of a plot against Chancellor Palpatine.
After his escape from prison with Cad Bane and Moralo Eval, the disguised Obi-Wan finds himself a fugitive pursued across the galaxy by Anakin himself, and must find a way to get the Jedi off their trail without blowing his cover.
Disguised as Rako Hardeen, Obi-Wan finds himself on Serenno and in the middle of a cut-throat competition to find the most skilled bounty hunters for Dooku's plot against the Republic.
Anakin and the Jedi work with their inside operative to try and thwart the Separatist plot to kidnap the Chancellor during a public appearance on Naboo.
Asajj Ventress returns home to Dathomir and rejoins the Nightsisters, but an angry Count Dooku orders a strike against Mother Talzin and her people -- leading to a catastrophic battle between Grievous's droid army and undead creatures raised to defend the planet.
Asajj Ventress joins a team of bounty hunters under the leadership of young Boba Fett, taking on a dangerous delivery mission where their cargo proves to be more than she expected.
Savage Opress goes in search of his lost brother, Maul, who he believes may have survived a fateful battle with the Jedi -- and is shocked by what he finds.
With his mind restored by Mother Talzin, Maul and Savage set out to exact revenge upon Jedi Master Obi-Wan Kenobi -- forcing Obi-Wan to join forces with Asajj Ventress in order to survive the powerful brothers.
