Geonosis has mostly fallen under Republic control, but Archduke Poggle the Lesser has evaded capture. Jedi Master Luminara Unduli is on his trail through a massive sandstorm that has grounded Republic ships and interfered with communications. Luminara and clone trooper Buzz track Poggle and his battle droids to the Progate Temple, which the Republic had thought cleared earlier. While searching the building, Buzz inspects a hole leading to the underground tunnels. Luminara calls in to inform Obi-Wan Kenobi and Ki-Adi-Mundi that Poggle appears to have entered the catacombs underneath the temple, when a scream is heard and the transmission cuts out.
After the sandstorm has ended, Anakin Skywalker, Obi-Wan, and Commander Cody arrive at the Progate Temple in order to search for Luminara. They find Buzz's body and Luminara's lightsaber and it's concluded that Luminara must have been taken below ground. The search party forms up and enters the tunnels.
The tunnels seem to stretch on forever, and there's no sign of Master Unduli — until Anakin and Obi-Wan get a brief message from her warning them to leave before she's taken down by some odd-looking Geonosians. Anakin and Obi-Wan decide to continue on, reasoning Luminara can't be far away. They are shortly attacked by a group of the odd-looking Geonosians, who they discover to be undead, kept mobile through some kind of parasitic control. They are extremely difficult to kill, and the search party eventually finds itself on the run. The Jedi decide they need reinforcements, and two clone troopers are sent to report back because they're so deep that their comm signals can't make it to the surface. They don't make it, attacked by the zombie Geonosians.
They eventually find their way to where Luminara is being held — the chamber of the Geonosian queen Karina the Great, whose existence was previously only rumoured. Karina wants to see if one of her brain worms can control a Jedi Master. The clone troopers position themselves around the edges of the room for an ambush and the Jedi walk straight in.
The ambush is sprung, Luminara is rescued, Poggle is arrested, and Karina is killed when the pillars supporting the ceiling of her chamber are shot out, causing it to collapse.
- Ancient Tomb: The tunnels beneath the temple are catacombs full of dead Geonosians.
- Badass in Distress: Luminara gets captured by the undead Geonosians at the Progate Temple and makes an escape attempt before she is rescued.
- Blinded by the Light: The ambush plan involves the clone troopers using the lights mounted on their helmets, as Karina and the zombie Geonosians spend all their time in the dark.
- Buried Alive: The clone troopers collapse the throne room on Karina, burying her and most of her zombies.
- The Cameo: Ahsoka, Barriss, and Rex appear at the beginning of this episode. The former two say goodbye to the latter.
- Chiaroscuro: The underground scenes are dark with dramatic shadows cast in the light from the clone trooper's helmets.
- Deadly Dust Storm: The sandstorm at the beginning grounds the Republic gunships and screws up communications, so help can't come immediately when Luminara goes missing.
- Glowing Eyes of Doom: The undead Geonosians have glowing white eyes.
- God Save Us from the Queen!: Karina is no less cruel and barbaric than the rest of her children.
- Hive Queen: Karina can control her subjects through the brain worms.
- Kidnapped from Behind: A number of clone troopers are dragged away from the squad through the many passages when their fellows are facing the other way.
- Killed Offscreen: Buzz, Luminara's clone companion, gets killed by geonosian zombies while his general was having a call with her fellow masters.
- Knight of Cerebus: The Geonosian zombies and Queen Karina's role in the episode foreshadows the Cerebus Syndrome that will affect the series after season 2.
- Nightmare Fetishist: Obi-Wan is way too curious about seeing if a brain worm actually could control Luminara. Anakin and Luminara call him on it. However, it turns out he was trying to get the guards to turn their attention away from him and Anakin so they could break free and rescue Luminara.
- Night-Vision Goggles: Yet again, we see the night vision feature on the clone troopers' helmets being used, prior to the ambush.
- Nose Art: The gunship Obi-Wan and Anakin take to the Progate Temple has a painting of a clone trooper's leg stomping a Geonosian and the nick-name The Bug Stomper.
- Not Using the "Z" Word: Averted. The undead Geonosians are explicitly called "zombies".
- Orifice Invasion: The Geonosian brain worms are shown slithering through the undead Geonosian's nostrils.
- Our Zombies Are Different: Insectoid Aliens controlled by parasitic worms? That's a new one.
- Puppeteer Parasite: The Geonosian brain worms are linked to a Hive Mind and controlled by the queen. They can even control Geonosian warriors after death.
- Shout-Out: The gunship that drops the team off at the Progate Temple is called The Bug Stomper.
- Skewed Priorities: Obi-Wan fakes being really interested in seeing if the Queen's plan to control Jedi will work in order to get her guards to ignore him and Anakin as a non-imminent threat. Later, while fleeing the throne room. Anakin yells at Obi-Wan when he does not immediately destroy one of the brain worms attacking him, as he wants to nab one for study. Anakin is of the opinion that the middle of a battle is the wrong time for such academic pursuits, throwing the worm to the ground and stomping on it before it can do any harm.
- Throw-Away Guns: During the escape from the catacombs, Commander Cody, holding up the rear, throws his blaster at the zombie Geonosians as he needs his hands free to climb the wall of the shaft leading up to the temple.
- Vertical Kidnapping: One of the Geonosian zombies grabs a clone trooper by the head and pulls him up to the ceiling to break his neck.
- With My Hands Tied: Luminara, while handcuffed, puts up a good fight against the undead Geonosians while attempting to escape.
- Writers Cannot Do Math: Eight clones, including Cody, are shown getting off the gunship with Obi-Wan and Anakin. Two get pulled screaming down small side tunnels in the first confrontation with the zombies, two more are killed when they separate from the group to try to contact General Ki-Adi-Mundi, but somehow there are five clones left when they get to the throne room when there should be four. The only way this works is if one of the clones who got dragged off earlier managed to survive, escape and make his way back to the group offscreen which seems like it should have been pointed out when he got back.
- Luminara's dinky little binoculars can apparently pick out a small crate 150 klicks (93 miles) away.
- The X of Y: "Legacy of Terror".