Naboo security forces discover a small battle droid presence in the Naboo plains. In a droid repair room, fragments of battle droids and a tactical droid recovered by security forces are under examination. Amidala finds it odd that the droid remains have such thick mud on them since they were supposedly found in the grasslands.

The Separatist tactical droid is temporarily reactivated and, at Padmé's prompting, Threepio tries to fish out any information about the droid's assignment on Naboo. It utters something about a virus, specifically about a leak of a small amount of virus from a secret laboratory.

At the same time, Jar Jar has been chasing a bright blue slug-beetle that has crawled out of one of the battle droid shells, and clumsily knocks over several shelves of spare parts. He explains that the tasty slug-beetle is one of his favorite delicacies, and it can only be found in one place on Naboo -- under the perlote tree in the eastern swamps.

The Naboo contact the Jedi Council, informing Yoda and Mace Windu of their discovery. Yoda agrees to dispatch two Jedi to investigate. Senator Amidala recommends Generals Skywalker and Kenobi. Yoda concurs. Padmé is determined to locate the laboratory.

Out in the Naboo plains, a shaak wrangler named Peppi Bow leads her herd to a river to drink. The shaaks at the stream suddenly collapse and die. Bow is distressed. The river has been poisoned.

A Naboo scout carrier sets down near the river, near the dead shaaks. Padmé and Jar Jar emerge in full bio-hazard suits and examine the dead animals. Peppi, unaware of their intentions, attacks them with her electropole. After making clear their peaceful intentions, Padmé learns from Peppi that whatever killed her shaaks isn't airborne. The poison is in the water.

Searching the eastern swamps, Padmé and Jar Jar are captured by battle droids and led into the underground laboratory where they are confronted by the diabolical Dr. Nuvo Vindi. He stands before a shielded cabinet filled with the infamous Blue Shadow Virus, a deadly plague wiped from the galaxy generations ago.

A Republic gunship lands at Theed palace, and Obi-Wan Kenobi, Ahsoka and Anakin Skywalker emerge. They are met by Typho, who reports that Padmé has gone missing in the swamps and that a geo-scan of her last coordinates revealed a vast underground laboratory.

With the help of Peppi Bow, Ahsoka locates the lab's south entrance. Anakin orders her to detonate charges at the entrance to serve as a distraction while he and Obi-Wan secretly enter the lab through hidden hatches.

Clone troopers led by Captain Rex rappel from their gunship into the breach that Ahsoka has made. She joins them. The other two gunships drop thermal detonators at the other hatches. Kenobi leaps into one, while Anakin jumps into another.

Anakin leads his troops into the laboratory, finding Vindi. He's got Padmé and Jar Jar tied to an electric terminal and offers the Jedi a choice: capture him, or save his friends. Vindi flips the switch on the electric terminal as he makes a dash for an escape tunnel. Anakin acts quickly to save Padmé and Jar Jar.

Anakin finds Dr. Vindi's secret hangar and cuts through his battle droid guards. To distract Anakin, Vindi throws a vial of the virus out the blast door. Anakin leaps to catch it while Vindi shuts the door behind the Jedi.

Padmé corners Vindi's assistant droid, who stole away with one of the plague-laden explosives. Jar Jar tackles it, dropping the bomb which Padmé catches. She radios her success to Ahsoka, who dispatches the bomb squad to Padmé's location.

Anakin and Obi-Wan cut their way into the hangar bay. Vindi drops a trio of vials from his rising platform, forcing Kenobi to break pursuit to catch them and make sure they don't break.

The hangar launch chute opens, streaming daylight into the hangar. Anakin leaps to the top of the platform and holds his blade at Vindi. Once more he tries to drop a vial, but he is tackled by Peppi, who knocks him down with her electropole.

Vindi cackles with glee because his timed bombs are ready to erupt. But there is no explosion. The clone troopers have deactivated all the bombs.