At a Republic staging area, wounded clones are being loaded into evacuation gunships. The next stage of the operation is up to Jedi Masters Luminara Unduli and Obi-Wan Kenobi. With Geonosian warlord Poggle the Lesser still at large, Unduli decides to seek him out on her own. 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 battered battle droids carries Poggle the Lesser and 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 studies a number of strategic charts and maps. Joined by Obi-Wan Kenobi, the two continue their search for Poggle the Lesser.

Luminara Unduli reports from the western deserts. She and clone trooper Buzz have spotted the dropped 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 by Republic forces. Anakin Skywalker, who has joined the Jedi on the transport bridge, warns Luminara of an incoming sandstorm.

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. Luminara has found the temple, and she and Buzz take refuge from the winds inside. Luminara contacts the Jedi transport with an update, and 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.

When the storm has cleared, a Republic gunship drops Commander Cody, his squad, Anakin and Obi-Wan at the Progate Temple. Cody finds Buzz's dead body, and Kenobi uncovers no trace of Luminara except 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 an unconscious Luminara into the heart of the catacombs. Poggle the Lesser leads them. Luminara awakens and kicks her way free, though her hands are bound by energy shackles. She wrestles her communicator free and hurriedly contacts Obi-Wan, warning him to abandon his search and leave while he can.

Her signal drops as she is overrun by the Geonosians. Kenobi presses on, realizing that she must be close by. Rounding a bend, the clones run into a horde of Geonosian warriors. The Jedi and clones attack, their blaster fire seemingly ineffective against the insects. 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. 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, Karina the Great, before whom Poggle the Lesser kneels. Anakin, Obi-Wan, Cody and the clones find the royal chamber but stay hidden, spying on the proceedings.

Kenobi and Skywalker emerge from the shadows while Cody and the clone troopers remain hidden. Obi-Wan 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.

As the worm slithers onto Luminara's skin, 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, escaping up an air shaft. A great geyser of dust pushes them to the surface, where they emerge shaken, filthy, but intact.