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.