"Blue Shadow Virus" marks the seventeenth installment in the first Season One of the animated television program Star Wars: The Clone Wars. Notably, it is also the seventeenth episode in the overall series. This episode serves as the initial segment of a special one-hour broadcast, which premiered on February 13, 2009.
Padmé, accompanied by Jar Jar and Threepio, arrives on Naboo, where they are greeted by Queen Neeyutnee and Captain Typho. The Queen insists that she must appeal to either the Senate or the Jedi High Council for assistance. Padmé counters that the evidence provided by a scout team of droids is insufficient, necessitating an analysis of the tactical droid captured during the scouting mission. After removing the droid's optical sensors, they deceive it into believing it is still aligned with the Separatists and instruct it to report. The droid manages to reveal the existence of a highly classified lab on Naboo before being inadvertently crushed by Jar Jar's clumsy actions while attempting to capture a blue bug emerging from a battle droid's chassis. It is determined that the bug could only have originated from the Eastern swamps, which is consistent with the mud found on the tactical droid. They establish communication with Master Yoda and Master Mace Windu, requesting the dispatch of two Jedi: Obi-Wan Kenobi and Anakin Skywalker. Subsequently, Padmé and Jar Jar decide to personally investigate the secret lab, while the others focus on extracting additional intelligence from the remaining droids.
In the open plains, a female Gungan shaak herder named Peppi Bow observes the sudden collapse and death of several of her shaaks. Realizing that the river they drank from is contaminated, she directs her herd away from the area. Shortly thereafter, Padmé and Jar Jar encounter Peppi, who initially attacks them until Padmé brandishes her blaster. Peppi advises them to follow the river to locate the source of the contamination and offers to guide them. However, Padmé declines, opting instead to request an escort back to Theed. As they navigate the swamp, they are unknowingly monitored by a surveillance camera. They eventually discover a concealed hatch, but lack the means to open it. Suddenly, they are ambushed by battle droids, subdued with stuncuffs, and transported to the lab. The facility's director, Dr. Nuvo Vindi, reveals that he has successfully recreated the Blue Shadow Virus, a highly virulent disease that had been eradicated from the galaxy long ago. Furthermore, he has refined the virus, converting it from a liquid form to an airborne strain, intending to use it to eliminate warmongers.
Upon their arrival on Naboo, Anakin, Ahsoka, and Obi-Wan are informed of Padmé and Jar Jar's independent investigation. Anakin dispatches Ahsoka, accompanied by Peppi, to locate them, while he and Obi-Wan analyze the data recovered from one of the lobotomized droids. They discover Vindi's plan to deploy virus bombs to strategically important star systems. Typho directs them to Vindi's clandestine lab, which has three possible entry points. Anakin expresses concerns about the risk of contamination, but Obi-Wan emphasizes that the potential loss of a single planet pales in comparison to the threat to the entire galaxy. Ahsoka and Peppi, while searching the swamp, inadvertently discover a hidden spy camera and manage to evade detection. Ahsoka communicates with Anakin and Obi-Wan, who instruct her to detonate an explosive device in the southern bunker while they infiltrate the lab through the hatches. Anakin then joins Rex and his clone troopers to commence the mission. Obi-Wan reminds Anakin that the safety of the galaxy outweighs Padmé's life, suggesting that she may already be deceased. Ahsoka uses the Force to levitate a thermal detonator, precisely dropping it onto the hatch, diverting the attention of numerous droids to her location. Rex and his team arrive to support her, engaging the droids in combat before being forced to retreat due to the deployment of droidekas. This allows Anakin and Obi-Wan to infiltrate the base undetected. However, upon entering Vindi's lab, Anakin finds Vindi subjecting his hostages to electric torture, forcing Anakin and his clones to surrender. As Vindi leaves Padmé and Jar Jar to suffer, he flees with his virus bomb. Anakin manages to free himself and rescue them. Obi-Wan arrives with the Bomb Squad. Unfortunately, as Obi-Wan and the bomb squad locate the bombs, Vindi activates them. With Vindi carrying a detonator and a droid carrying an armed bomb, they divide their efforts. Obi-Wan attempts to apprehend Vindi, but the villain releases several virus vials, forcing Obi-Wan to prioritize containing them while Vindi escapes. Meanwhile, Padmé and Jar Jar pursue the droid, successfully preventing its escape. With the assistance of the bomb squad, they manage to deactivate all the bombs just as they capture Vindi.