"Sometimes, accepting help is harder than offering it."
Victory on Geonosis! After a massive planetary siege, the Separatist forces on Geonosis have finally fallen. Key weapons factories have been destroyed, but at a heavy cost to Republic troops. Now, as Jedi Master Luminara Unduli and Obi-Wan Kenobi begin a clean-up of the planet, they launch an intense campaign to find Separatist leader the Lesser and bring him to justice.
At a Republic staging area, wounded clones are being loaded into evacuation gunships. One such gunship ferries exhausted Padawans Ahsoka Tano and Barriss Offee away for much needed recuperation after their ordeal of destroying the primary droid factory. The next stage of the operation is up to Jedi Masters Luminara Unduli and Obi-Wan Kenobi. Overlooking the camp, Kenobi reports that no sign of Poggle the Lesser has been found, but clone scouts are spread throughout the desert, searching for clues. Showing an impetuous streak, Unduli decides to seek out Poggle on her own. The Geonosian warlord has too much information about the Separatists to escape. She climbs aboard a BARC speeder and zips off into the wastes.
Deep in the desert, a lone, battered AAT assault tank loaded with three worse-for-wear battle droids carries Poggle the Lesser and a retinue of two royal guards. The tank tows several crates of munitions. A bump in their path causes a box to fall behind, but Poggle orders to keep pressing forward.
Aboard a Jedi transport resting at a Geonosian landing zone, Ki-Adi-Mundi has recovered from his injuries and consults a number of strategic charts and maps. He is joined by Obi-Wan Kenobi, who is happy to see the Cerean Jedi Master up and about. Poring over the remotely gathered data, they continue their search for Poggle the Lesser.
Luminara Unduli reports from the western deserts. She and clone trooper Buzz have spotted the wayward munitions container in the middle of nowhere. Buzz estimates that whoever dropped the case was headed straight for the Progate Temple, a site of heavy bombardment during the initial Republic siege. The Jedi puzzle over why Poggle would head to such a ravaged area, but Luminara wastes little time on speculation. Anakin Skywalker, who has joined the Jedi on the transport bridge, warns Luminara of an incoming sandstorm. Unduli is not frightened off by inclement weather -- rather, she is motivated to catch Poggle all the more.
The choking cloud of dust has already consumed Poggle's escape tank. One of the hapless battle droids disappears in the sands. Poggle nonetheless continues to press on. Luminara and Buzz can't spot Poggle in the storm, but they keep their bearing toward the Progate Temple.
Back at the Jedi transport, Kenobi, Ki-Adi-Mundi and Skywalker are stranded by the harsh winds, and try not to worry too much about their sandbound compatriot. Luminara has found the temple, and she and Buzz dismount their speeders and take refuge from the winds inside the temple ruins marked by creepy icons. Luminara contacts the Jedi transport with an update. Kenobi advises her not to proceed further until the storm lets up and the Jedi can provide backup. But Buzz spots an entrance to an underground cavern.
Luminara reports that Poggle has gone into the catacombs. Her hologram is suddenly cut short as Buzz screams at something, and she ignites her lightsaber. The Jedi in the transport are left to fear the worst. Skywalker is determined to go to her, but he must wait for the storm to lift. The gunships will not handle the whirling dust.
The storm has cleared, and a Republic gunship deposits Commander Cody, his squad, and the Jedi Anakin Skywalker and Obi-Wan Kenobi at the Progate Temple. Cody finds Buzz's dead body, and Kenobi uncovers no trace of Luminara save for her lightsaber. Anakin doesn't believe Poggle could have defeated a Jedi. Upon seeing a grotesque statue of a bizarre Geonosian, Obi-Wan speculates that perhaps it was the long rumored Geonosian queen, of whom no evidence had ever been discovered.
The clones and the Jedi enter into the caverns, their lightsabers and helmet lamps illuminating the way. Cody's wrist-mounted tracker points to the tunnel that penetrates deepest into the planet's crust.
Meanwhile, oddly affected Geonosian guards drag the inert form of Luminara into the heart of the catacombs. The glassy eyed drones stagger as they follow Poggle the Lesser. Luminara awakens and kicks her way free, though her hands are bound by energy shackles. She lands a heavy blow that breaks into a Geonosian's thorax, but the creature doesn't fall. Luminara wrestles her communicator free and hurriedly contacts Obi-Wan. She warns Kenobi to abandon his search and leave while he can.
Her signal drops as she is overrun by the Geonosians. Kenobi doesn't heed her words, and instead presses on, realizing that she must be close by. Rounding a bend, the clones run into a horde of Geonosian warriors. The squealing insects swarm them, forcing the troops to open fire and the Jedi to attack with their lightsabers. The blaster fire cuts into the Geonosians, but they do not fall, despite taking what appear to be lethal wounds. In the blink of an eye, a clone trooper spots a strange, bright green worm flicker through a Geonosian's nasal cavity during the fight.
Outnumbered, Kenobi orders a retreat. The clones blast the tunnel supports, collapsing the caverns on top of the relentless Geonosians. Anakin is bewildered by the aliens' tenacity. Kenobi has heard rumors of a Geonosian hive mind so powerful, that it can even animate the dead. This deep in the caverns, the Jedi cannot get a comlink signal, so Kenobi orders two clones to backtrack to the surface and contact Ki-Adi-Mundi for reinforcements. They do not get very far before being killed by Geonosian zombies.
In the central hive, Luminara awakens to find herself pinned in a Geonosian energy trap. She sees the undulating egg-sac of the enormous, hideous Geonosian queen. Anakin, Obi-Wan, Cody and the clones find the royal chamber, where Poggle the Lesser kneels in supplication to Karina the Great. The intruders stay hidden, spying on the proceedings. Anakin is set to attack, but Kenobi wants answers. He wants to know what the Geonosians are up to.
Kenobi and Skywalker emerge from the shadows while Cody and the clone troopers remain hidden. Obi-Wan begins a dialogue with the Queen, while Anakin is ready for action. Kenobi orders the release of Luminara, who is surprised to see the Jedi. The shrieking Queen Karina refuses to recognize the Jedi's authority. She wishes not to destroy the Jedi, however. She desires to control them. Kenobi watches, captivated, as one of the Geonosian zombies carries a small egg in his hand. From it emerges a wriggling worm -- the instrument of the Queen's mind control.
Kenobi takes no action until the worm is released to crawl upon Luminara's skin. He wants to capture the creature alive to study. Only once it slithers on Luminara do Kenobi and Skywalker strike. Obi-Wan orders Cody to attack. The clones snap on their helmet lamps, temporarily blinding the dark-dwelling Geonosians. Anakin cuts through Luminara's bonds and slaps shackles on Poggle. In the scuffle to escape, Anakin knocks the worm from Obi-Wan's grip, and crushes it under his boot.
The clones blast the chamber supports, bringing tons of rubble crashing atop the Queen and her zombies. The Jedi, clones, and the bound Poggle run from the chaos, clambering up an air shaft. A great geyser of dust pushes them to the surface, where they emerge shaken, filthy, but intact.