R2-D2 is lost during a fierce space battle -- and Anakin must find him before the Separatists discover the Jedi military secrets locked in his memory banks.

Anakin, Ahsoka and replacement droid R3-S6 embark on a dual rescue/sabotage mission when they discover R2-D2 is being held at General Grievous' secret enemy listening post, Skytop Station.

Anakin and Ahsoka arrive at a pitched sky battle to help besieged Jedi General Aayla Secura. Anakin is gravely injured in the fight. Aayla and Ahsoka, along with the now-wounded Anakin, Rex, and the surviving clones, crash land on the uncharted grass-covered planet, Maridun. Forced to leave Anakin behind in order to save him, Aayla teaches Ahsoka why the Jedi have no personal attachments. They make their way to a Lurmen village. Their ruler, Tee Watt Kaa, explains that they're pacifists in this war and are not aligned with either side. Hesitant to have anything to do with the Jedi, Tee Watt Kaa agrees to help save Anakin's life.

The battle for the Twi'lek homeworld of Ryloth rages as the Republic attempts to drive off the occupying droid army led by Separatist Leader, Wat Tambor. With his forces stretched thin, Mace Windu must convince Twi'lek freedom fighter, Cham Syndulla, to help him save the capital city from the droids' destruction. Initially, the Twi'lek hero is hesitant to aid Mace, but ultimately realizes the Jedi can be trusted and joins with him to liberate the city -- and ultimately the planet -- in the climactic battle.

Anakin and Ahsoka travel to the planet Devaron in pursuit of Cad Bane, who has stolen a Jedi holocron. Bane has captured Jedi Master Bolla Ropal, keeper of the Kyber crystal, which will reveal data on every known Force-sensitive child in the galaxy when combined with the holocron. Failing to force Ropal to open the holocron, Bane needs another Jedi. Capturing Ahsoka, the bounty hunter forces Anakin to open the holocron to save his Padawan. The holocron's secrets revealed, Bane attempts an escape, but appears to be killed by a clone. Anakin, however, still senses Bane's presence in the Force...