Anakin Skywalker and the rest of his Jedi team have been overrun by the Separatist surprise attacks led by Riff Tamson while Prince Lee-Char and Ahsoka must evade capture on their own. Unable to summon more Republic aid, Yoda calls upon the help of the powerful and amphibious Gungan Grand Army, but whether they will be enough to stop the Separatist siege is uncertain. An incensed Tamson doubles his efforts in tracking down Prince Lee-Char, unleashing the reinforcements given to him by Count Dooku in an assault that churns the oceans.

The Republic and Gungan forces have been captured by Riff Tamson and his Karkarodon enforcers. Now, it is up to Ahsoka and the young Prince Lee-Char to unite the fractured people of Mon Cala and drive out the Separatist invaders.

When the leader of the Gungans, Boss Lyonie, is injured it's discovered there is an uncanny resemblance between the Boss and Jar Jar Binks. Binks must sway his people from rising against the Naboo and stopping a Separatist invasion led by General Grievous.

After groundquakes have devastated the planet Aleen, a Republic relief effort arrives, including the droids R2-D2 and C-3PO. When the native Aleena's pleas go unheard, it becomes the duty of the droids to embark on a surreal journey through Aleen's subterranean world to save the planet.

C-3PO and R2-D2's bizarre caper continues. Forced to escape a Separatist attack in a Y-wing fighter, the droids visit the world of the Patitites, the odd planet Balnab, and the inside of a pirate warship where they are forced to fight in a gladiatorial arena.

When Anakin is forced to temporarily turn over command of his clone troopers to a new commander, the Jedi Pong Krell, tensions begin to run high as the clones are assigned with a very deadly mission to take the capital of Umbara.

General Krell orders Captain Rex and the clone troopers of the 501st Legion to conquer a heavily fortified Umbaran airbase, and will not accept anything less than victory. It is an almost certain suicide mission, unless the clones can use their ingenuity to defeat their new enemy.

After the Republic conquers an Umbaran airbase, General Krell orders Rex and his men on towards the heavily fortified capital. Realizing there's a better plan, several clone troopers disobey orders to carry out a rogue, covert operation.

With two of his men facing execution for disobeying orders, Captain Rex must confront his overly aggressive commander, General Krell. Risking charges of mutiny, Rex must make a dark choice as the true face of the enemy emerges.

Zygerrian slavers are behind the sudden disappearance of an entire colony of people on the planet Kiros. As Anakin and Ahsoka rush to defuse a series of bombs planted by the slavers, Obi-Wan must fight with their imposing leader.

To locate the missing colonists, Anakin, Obi-Wan and Ahsoka go undercover to infiltrate the slavers on Zygerria. Anakin struggles with his emotions as a wily Zygerrian queen forces him to take questionable actions in order to carry out his mission.

Anakin tries to convince the Zygerrian Queen that she too is a slave and pawn in an evil Separatist plot. Meanwhile, Obi-Wan toils in the slave camps of Kadavo, a grim situation that grows increasingly bleak.

A peace conference between Separatists and Republic delegates is interrupted by Lux Bonteri, the son of a late Separatist Senator, who involves Ahsoka in his dangerous search to find justice for his mother's death.

When the Jedi learn of a Separatist plot to kidnap Chancellor Palpatine, one of them must go deep undercover as a hardened criminal to extract information from the conspirators.

Fleeing across the galaxy with criminal fugitives, a disguised Obi-Wan, Cad Bane and Moralo Eval are tenaciously pursued by Anakin and Ahsoka, who have no idea they're chasing their friend.

The disguised Obi-Wan accompanies Cad Bane and Moralo Eval to Serenno, where they enlist in a brutal competition with other bounty hunters from around the galaxy to determine who will participate in a plot to kidnap the Chancellor.

The Chancellor travels to Naboo to preside over a public ceremony, guarded by Jedi Knights. Dooku and his bounty hunters -- including an undercover Obi-Wan Kenobi -- launch their kidnapping plot.

Count Dooku is determined to have revenge against the Nightsisters of Dathomir after their betrayal. General Grievous launches an all-out droid attack against the magic-wielding witches, and Mother Talzin and Asajj Ventress lead the defense with all the dark powers at their command.

An aimless Asajj Ventress joins a team of bounty hunters under the leadership of young Boba Fett. On an alien world, they undertake a dangerous but profitable mission that tests the limits of their skills, and the strength of Asajj's character.

Savage and Maul, now reunited, pursue Obi-Wan Kenobi in search of revenge, and the Jedi Knight finds himself forced to unite with a surprising ally to defend against the deadly siblings.