Padawans Ahsoka Tano and Barriss Offee are selected to transport medical supplies to Mace Windu on Dantooine from a station near Ord Cestus, while Obi-Wan Kenobi, Anakin Skywalker, Luminara Unduli and Ki-Adi-Mundi prepare to deliver Poggle the Lesser to Coruscant. At the same time, a group of clone troopers are resting outside the Progate Temple, where a brain worm hatches from its egg and enters into the nose of one of the troopers, Scythe. Moments later, the company is awakened and informed of their new errand mission to Ord Cestus. They follow the Padawans aboard the medical frigate TB-73, with Scythe at the rear carrying more brain worm eggs in his backpack.
After the frigate jump into hyperspace, Ahsoka and Barriss lie in their beds, but Ahsoka can’t sleep. She thus suggests to Barriss that they should go eat, and they head off to the mess hall. Meanwhile, Scythe enters the troopers’ sleeping quarters and releases some of the yellow eggs; the worms hatch and find their way into the noses of the sleeping clones. While the Padawans are eating, Scythe leads two infected clones to kill the ship’s pilots, taking control of the bridge. Two other possessed clones enter the mess hall and attack the Padawans, who eventually manage to knock the troopers unconscious. An instant later, two more clones, Trap and Havoc, come through the door. The Jedi question them with lightsabers drawn, but the troopers say they don’t know what is going on, and put their guns on the floor. The Padawans then deactivate their lightsabers, and the four of them decide to check if they are still in control of the bridge. After Barriss fails to contact the bridge via comlink, the two Padawans and Trap set off to go there, while Havoc stays to watch the unconscious clones.
In a different place in hyperspace, Jedi Masters Luminara and Ki-Adi inform Anakin and Obi-Wan that the medical frigate did not check in on time. Anakin starts to worry for Ahsoka, but Ki-Adi suggests they should focus on interrogating the so far uncooperative Poggle.
Concurrently, the infected clones aboard the medical frigate engage the autopilot and security shields, blocking the way for Ahsoka, Barriss and Trap. Barriss tries to override the shield controls, but Trap then fires his blaster at her. She manages to deflect it and disarm him, noticing that he too is infected by a brain worm. He throws himself at her, and she ultimately has to kill him in self-defense. Ahsoka manages to kill the brain worm which has emerged to take possession of Barriss.
The Padawans decide to contact Master Fisto and quarantine the ship, but on their way they come across the cargo hold, where the infected troopers are releasing a brain worm into another trooper. They are spotted and realize they are outnumbered, so they escape through the ventilation system. From there, Barriss goes to disable the thrusters, and Ahsoka heads to the communication room to send a warning to Kit Fisto. Ahsoka tells Fisto about the worms, but he insists that the frigate docks anyway in order for the worms to be taken out by a sanitation team. Ahsoka also contacts Anakin, updating him on the situation.
On her way to the reactor, Barriss gets temporarily incapacitated by an electric trap and is exposed to a newly hatched brain worm by the troopers. After finishing her transmission, Ahsoka is surprised to see Barriss standing beside her. The possessed Barriss attacks her, and after a brief fight, Ahsoka manages to escape into the ventilation system.
In the meantime, Anakin angrily goes to interrogate Poggle, using the Force to try to make him talk, but this doesn’t work; he thus hits Poggle and proceeds to Force choke him. After getting the information he needs, Anakin informs the other Jedi about the brain worms, contacts Ahsoka on her comlink and tells her that the worms are affected by cold temperature, and that she should rupture the coolant system. She does this, releasing freezing air into the ship, just as it comes out of hyperspace. While the clones get weakened by the cold, Barriss finds Ahsoka’s trail again and confronts her inside the bridge. They fight, but Barriss and her worm are eventually taken out by the cold. Regaining her own will for a moment, Barriss begs Ahsoka to kill her, but Ahsoka can’t bring herself to do so. Barriss attacks again, but Ahsoka manages to kill the worm as it protrudes from Barriss’s mouth.
The frigate docks at the station, and Kit Fisto boards it with two clone troopers. They find the two frozen Padawans lying on the ground, still breathing, and brings them to the infirmary. When Ahsoka wakes up, Anakin is waiting at the end of her bed, and assures her that everything is alright, and that Barriss and the troopers were saved. Fisto explains the parasite's origins, and he and Anakin theorize this was likely how the Geonosian recaptured their planet: Anakin remarks the troops of Geonosis will have to be warned, so such an incident doesn't reoccur.
Once Fisto has left, Ahsoka tells Anakin about Barriss begging for death under the worm's influence, and wonders if she should have killed Barriss, since had they failed, her refusal could have resulted in the entire medical station being infected. Anakin consoles her with the knowledge Barriss only thought her death was necessary to stop the worms, and that she did the right thing in sparing her friend, since it is a Jedi's responsibility to save as many people as they can.