Mystery of a Thousand Moons

The deadly Blue Shadow Virus has been unleashed, resulting in the infection of Ahsoka, Padmé, and numerous Clone Troopers. This dire situation leaves Anakin and Obi-Wan with a mere 48 hours to locate the antidote on an enigmatic planet from which no traveler has ever successfully returned.

Obi-Wan and Anakin make preparations to move Dr. Nuvo Vindi to Theed for his impending trial. Padmé and the clone troopers discover that a container that held the Blue Shadow Virus is missing from one of the virus bombs. This implies that the virus can still be deployed if it falls into the wrong hands (as is the case with Vindi), prompting them to raise the alarm.

Two clone troopers are searching the bomb room for Vindi's servant droid. The droid secretly enters the room behind them and proceeds to insert the virus into one of the bombs. Before the clones are able to intervene, the droid detonates the bomb, causing the virus to rapidly spread throughout the complex. Rex, Ahsoka, and the clone troopers successfully manage to reach the safe room. Ahsoka informs Anakin about the virus's release, and he subsequently informs Padmé. Padmé, accompanied by Jar Jar and wearing their EVA suits, sets out to locate Ahsoka and prevent any remaining droids from escaping the lab and releasing the virus onto the planet.

Anakin attempts to extract the antidote from Vindi, but Vindi mocks him, asserting that his role was to create a plague, not to develop a cure. Obi-Wan manages to persuade Anakin to put down his lightsaber, and they leave for Theed. Ahsoka, Rex, and the clone troopers realize that a small amount of the virus entered the safe room before the door was sealed, resulting in their contamination. Padmé and Jar Jar, having been summoned by Ahsoka, open the door to the safe room. Padmé and Ahsoka then undertake the mission of destroying the droids before they can reach the surface of Naboo. During a struggle within one of the corridors, Padmé disconnects a hose from her EVA suit after tackling Jar Jar to prevent him from attempting to shoot Destroyers with their shields active. This action could potentially injure or even kill Ahsoka, who is on top of the droids, destroying them through the weak points in their shields, and is therefore vulnerable to the virus.

Anakin, Obi-Wan, and Vindi arrive in the hangar bay, where they encounter Typho. Vindi is escorted away, and Typho informs Anakin and Obi-Wan that he may have discovered an antidote: Reeksa root, which is exclusively found on Iego, the World of a Thousand Moons, located within Separatist-controlled territory. Typho describes the mission as "suicide", but Anakin and Obi-Wan nevertheless depart in the Twilight.

As Anakin and Obi-Wan approach Iego, they must navigate through a massive graveyard of ships orbiting the planet. Upon landing, they encounter strangely deformed droids with mismatched parts, all repeating the phrase, "Welcome to Iego". A boy approaches them, introducing himself as Jaybo, before relaxing in a hammock suspended between the legs of two Vulture droids, attended to by retrofitted battle droids. Jaybo explains that when the Separatists departed, they abandoned many of their droids, which he subsequently reprogrammed to serve him. When Obi-Wan and Anakin inquire about the Reeksa root, Jaybo mentions that the system is "haunted" and that no one ever leaves the planet because Drol, the phantom ruler of Iego, destroys anyone who attempts to escape. According to Jaybo, fifty of the galaxy's best pilots have tried, but none have survived.

Anakin and Obi-Wan descend a cliff, while Jaybo warns them not to touch the vines, as the plants "don't like it" and possess large, sharp teeth. A Xandu appears, and the two Jedi seize it. The Xandu transports Anakin and Obi-Wan to the bottom of the cliff, where Anakin begins to cut away a portion of a root, causing the Reeksa plant to awaken. Anakin and Obi-Wan successfully fend off the Reeksa and ascend the cliff.

Jaybo leads them to Amit Noloff, who informs the Jedi that the ghost of Drol is preventing them from leaving the planet. When the Jedi express disbelief, he shows them a hologram of Taquito, a friend of Jaybo's, being electrocuted before his ship exploded. Anakin and Obi-Wan attempt to depart Iego in the Twilight, but as they pass through the debris field, sensors activate a network of electrical lasers that prevent them from venturing far from Iego, forcing them to return. The ghost of Drol turns out to be an energy field that Obi-Wan theorizes the Separatists installed as an electric fence to prevent the inhabitants from leaving the planet.

Upon landing, Obi-Wan and Anakin receive a hologram from Ahsoka and Padmé, both appearing dehydrated and weak. Ahsoka weakly informs them that they have destroyed all the droids in the compound and that Naboo is safe from further contamination. Padmé asks Anakin to promise her that no one will ever open the bunker, and begins to say "I love you", but the hologram is abruptly cut off. As they step onto the platform, Anakin begins to panic, realizing that Ahsoka and Padmé are succumbing to the effects of the virus. He attempts to rush and find a solution to bypass the energy field, but Obi-Wan devises an idea and manages to calm Anakin down.

The Jedi convene a meeting with the citizens of Iego. Obi-Wan informs them that Drol is not a ghost, but a Separatist security system. He asks if anyone inhabited Iego's moon before the Separatists arrived, and an Angel enters the room. She tells the Jedi that they were a peaceful people before the Separatists arrived and stole their home: the moon of Millius Prime. Anakin theorizes that the primary node of the energy field must be located near Millius Prime. Obi-Wan notices Vulture droids in another room and asks Jaybo to reactivate them so that Artoo can fly them via remote control. The Vultures are activated, and after Jaybo transfers control of the droids to Artoo, they launch and follow the Twilight into the ship graveyard. The laser field activates, and Artoo attempts to send the Vulture droids into the laser emitter, but they are destroyed. Obi-Wan fires at the generator, causing the energy field to explode. Anakin mentions to Jaybo that he will need new Vulture droids, as all were destroyed, but Obi-Wan informs them that they are now free to leave Iego whenever they choose. The Twilight immediately jumps into hyperspace for Naboo.

Meanwhile, in the lab, Padmé and Jar Jar are tending to the clones. Witnessing the clones succumbing to the virus, Padmé laments the waste of life. Rex responds that this is what these men were born to do. Padmé expresses her hope that their sacrifice will bring them closer to peace. Ahsoka begins to agree, but faints. Fortunately, Rex catches her, preventing her from being injured, but her friends are alarmed, fearing that the young padawan may not survive.

LAAT/is land at the lab, and stretchers carrying Padmé, Ahsoka, Rex, and the remaining clones are transported onto the gunships. Anakin and Obi-Wan find the others weakened from their ordeal, but thanks to the antidote, they are expected to make a swift recovery. Pleased with the outcome, everyone commends each other for their accomplishments.

This episode marks a first for the entire series, as it does not have a corresponding web comic on StarWars.com leading into it, as it directly follows the events of the previous episode.

Originally, the Xandu was intended to be consumed by the Reeksa plant.