At a landing area on Geonosis, clone troopers march a manacled Poggle the Lesser aboard a waiting shuttle. The Jedi receive news that the Republic desperately needs medical supplies delivered from Ord Cestus to the battlefront on Dantooine. Anakin Skywalker and Luminara Unduli feel it's of paramount importance to take Poggle to Coruscant instead. They decide to split their forces and have the Padawans, Ahsoka Tano and Barriss Offee, ferry the medical supplies.

The off-duty clone troopers of Tango Company nap outside the Progate Temple ruins. A slimy Geonosian brain worm slithers from an egg in the ruins, and crawls into the nostril of Scythe, a snoozing clone. The company C.O., Trap, wakes his resting soldiers since they've been assigned the medical run to Ord Cestus.

As the company boards medical frigate TB-73, Scythe lags behind, secretly carrying a backpack full of worm eggs aboard. The frigate blasts off from Geonosis, destined for Ord Cestus, where Kit Fisto is stationed, awaiting its arrival.

Deep in hyperspace, the Padawans attempt to catch some sleep, but Ahsoka is restless. She wakes Barriss, and they dine in the mess hall, talking about the Jedi's role as warriors in the current conflict, and how the Jedi will continue to maintain the peace after the war is over.

Meanwhile, in the clone barracks, Scythe has released a clutch of Geonosian brain worm eggs, which hatch and release their slithery bounty into the sleeping quarters. Each worm soon finds a sleeping clone host. The infection is spreading; two brain-washed clones led by Scythe casually walk into the cockpit and open fire on the pilots. They now have control of the bridge.

Two other infected troopers -- Ox and Edge -- enter the mess hall and suddenly open fire on Barriss and Ahsoka. The Padawans spring into defensive mode, deflecting the incoming blasts. They incapacitate the clones. Before they can assess the situation, the Padawans suddenly react as two more clones -- Trap and Havoc -- barge in, investigating the sound of gunplay.

These new arrivals do not appear infected, but Ahsoka and Barriss hold them at lightsaber-point until they can get some answers. Trap is just as confused as the Jedi. He drops his blaster to the floor to prove he isn't a traitor. Trap suggests they check on the bridge. Barriss cannot make comlink contact. Leaving Havoc behind to watch the two unconscious clones, Trap, Barriss and Ahsoka dash to the bridge to investigate.

The possessed clones engage the autopilot, and activate the security shields throughout the ship. Ray shields suddenly cut off the Padawans' approach to the bridge. Suddenly, Trap tries to blast Offee. She cuts through his blaster, and he struggles to overpower her. A Geonosian brain worm extends from his mouth. Barriss has no choice but to plunge her blade through Trap's chest, killing him. Ahsoka slices the worm in two with her lightsaber.

Looking at the wriggling segments, Ahsoka and Barriss begin to piece together what is happening: a parasitic infection is threatening the ship. The frigate must be placed under quarantine, and the medical station at Ord Cestus needs to be contacted. Barriss and Ahsoka overhear the chittering sound of Geonosian-speak. They follow the noise to the medical frigate's cargo bay.

There, they see infected clones -- including Scythe, Havoc, Edge and Ox -- gather and subject another trooper to the worms. An infected clone trooper spots the Padawans, herding the spies into the cargo bay. Havoc tosses two eggs at the Jedi, but they cut the orbs into halves before the worms can emerge. Outnumbered, Ahsoka and Barriss retreat into the ventilation ductwork.

Crawling through the ship's innards, Barriss and Ahsoka decide to split up. Offee goes to the reactor room to disable the ship's thrusters. Ahsoka heads to the aft communications station, and reaches Master Fisto with a warning. Kit Fisto orders Ahsoka to bring the frigate in-system so that the Jedi can analyze the parasites, but Ahsoka stresses how dangerous these worms are.

Barriss never reaches the reactor control room, instead getting caught in an electrified trap set up by the clones. She collapses before them. Scythe has an egg for her. She too becomes infected.

Back in the communications station, Ahsoka reaches Captain Rex and Anakin. She updates her Master on what's happening. Skywalker orders Ahsoka to keep in touch, while he goes to interrogate Poggle for some answers. But before Ahsoka can leave the comm room, Barriss attacks her. Both Jedi apprentices ignite their lightsabers, and an intense duel ensues. Ahsoka kicks her way free and leaps into the ductwork, momentarily escaping.

Aboard the Jedi cruiser, an intense Anakin Skywalker enters Poggle the Lesser's detention cell. Anakin excuses the clone guards, and attempts to use the Force to compel Poggle to answer his questions. Poggle, talking via an interpreter droid, boasts that mind tricks do not work on Geonosians. But Anakin is not looking to use mind tricks -- he smacks Poggle aside, and begins throttling him with a Force grip.

Skywalker contacts Ahsoka with the solution to the parasite problem: the worms are affected by extreme cold. Following her master's advice, Ahsoka heads to the reactor room to rupture the cooling system. Cold air begins flooding the frigate. The infected clones begin falling unconscious, gripped by convulsions.

The frigate emerges from hyperspace near the Ord Cestus medical station. Kit Fisto orders a pair of tug ships to guide in the stricken craft, and warns all medical staff that no one is to board the frigate until all parasites are contained. The tiny tugs attempt to rein in the frigate with their outsized tractor beam projectors.

Shivering in the corridors, Ahsoka returns to the bridge to retake control of the craft, but Barriss finds her. Their duel slashes a cooling duct, and Ahsoka blasts a jet of frosty air right at Offee. In that brief instant, Offee appears to surface from her worm-controlled haze, and begs Ahsoka to kill her.

The tugs reel in the frigate, halting its forward momentum just as it nestles into the medical station dock. Subzero conduits connect to the airlocks, and cautious clone troopers board the frozen craft, accompanied by Kit Fisto. Master Fisto sees the inert forms of Ahsoka and Barriss covered in frost. Ahsoka awakens in the infirmary and sees Anakin looking over her. He tells her that Barriss and the clones are fine, thanks to her efforts.