With help from R2-D2 and a squad of captured battle droids, an elite team of Jedi and clone troopers led by Obi-Wan and Anakin attempt to free a captive Jedi general, Even Piell, from an impenetrable prison. Despite orders to the contrary, Ahsoka Tano tags along, though she proves indispensable when the infiltration mission begins to evolve. Piell and his fleet officer, Captain Tarkin, are liberated from their cells, but now the fugitives must escape the Citadel itself.

With freed prisoners in their possession and the brutal warden attempting desperately to thwart them, Obi-Wan and Anakin search for a way out of the Citadel and back to Coruscant. The prison, however, has more traps, perils and pitfalls in store for them than they had imagined and they must work past their differences if they are to escape. Their bid to board their shuttle fails when heavy weapons fire destroys the escape craft. Trooper Echo dies in the blast. The escapees then flee to the caves and call for rescue from the Jedi Temple on Coruscant.

After their ship and only way off the planet is destroyed, Anakin and Obi-Wan must lead the escaped prisoners across Lola Sayu's perilous landscape as Plo Koon commands a task force of four cruisers and their fighters through the Separatist defenses in a daring rescue. Even Piell is ravaged by anooba tracking beasts, but before he dies, he passes on his Nexus Routes coordinates to Ahsoka. When the survivors return to Coruscant, Ahsoka knows half the intel, and refuses to disclose it to anyone but the Jedi Council, while Tarkin refuses to hand over his half to anyone other than the Chancellor.

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.

The clones look to uncover the source of the Separatists' strategies...and bring in an elite squad called the Bad Batch.

Rex, Anakin, and the Bad Batch look to uncover the truth surrounding a mysterious Separatist signal.

Rex has found his friend, Echo, in the clutches of the Techno Union. But the rescue is just beginning.

While Jedi Mace Windu and Obi-Wan Kenobi lead an attack against the Separatist forces on Anaxes, the Bad Batch and Anakin Skywalker infiltrate an enemy starship to ensure a Republic victory.