Battle droids on Naboo! As theSeparatist rebellion rages throughthe galaxy, even peaceful planets arethreatened. Following the discoveryof Separatist droids wandering the grassywasteland, Naboo is once again onhigh alert. Fearing their home is facinganother invasion, Senator Amidala andRepresentative Binks race to Naboo toassess the situation. Meanwhile, nearthe Gungan swamplands, an even graverthreat is about to be discovered....
The gleaming Naboo yacht lands within the cavernous Royal Hangar at the Theed Palace on Naboo. Awaiting its arrival are Queen Neeyutnee, the current Naboo monarch, and Captain Typho. Senator Padme Amidala, Jar Jar and C-3PO hurry out of the craft and meet with the queen, who reports that Naboo security forces discovered a small number of battle droids in the plains. Neeyutnee wants Amidala to inform the Senate that Naboo is threatened, but Amidala knows the Senate will require more proof.
They retire to a droid repair room, where the fragments of battle droids and a tactical droid 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. Jar Jar is distracted. He smells something that causes him to poke around the banks of spare parts. Meanwhile, a medical droid begins a robolobotomy on the tactical droid, poking around its memory banks to see what it can find.
The droid springs to life, though its photoreceptors are not functional. At Padme's prompting, C-3PO lies to the droid, telling it that it is aboard a Separatist ship. 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. The droid comes to realize it has been duped and clams up. 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. The chaos litters debris everywhere, and disrupts the robolobotomy, shorting out the tactical droid.
Jar Jar humbly apologizes. 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. Jar Jar has unwittingly pointed the way to where the secret laboratory might be.
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. Padme is determined to locate the laboratory.
Out 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 soars over the plains towards the eastern swamps. It sets down near the river, near the dead shaaks. Padme and Jar Jar emerge in full bio-hazard suits and examine the dead animals. Peppi, unaware of their intentions, attacks them with her electropole. She yanks off Jar Jar's helmet, and is surprised to see a Gungan underneath. Padme holds her at gunpoint, trying to get her to calm down. Jar Jar panics without his helmet, but Peppi explains that whatever killed her shaaks isn't airborne. The poison is in the water.
Padme explains they are trying to make their way to the perlote trees. Realizing their intentions are pure, Peppi volunteers to guide Padme and Jar Jar, but Padme tells her to stay here. It's too dangerous. Amidala will dispatch Naboo guards to take her back home.
Later, in the thick of the eastern swamps, Padme and Jar Jar look for anything out of the ordinary. A stalk-mounted photoreceptor emerging from the swamp ground watches them. Observing them from underground is the strange Dr. Nuvo Vindi, the diabolical mastermind behind this Separatist plot. Vindi orders battle droids to the surface to capture these interlopers.
Jar Jar's bumbling uncovers a metal surface beneath the swamp soil -- it appears to be a hatch. Padme radios Captain Typho, requesting a geo-scan of coordinates SP127. Battle droids suddenly emerge from the swamps and hold Jar Jar and Padme at gunpoint.
Jar Jar and Padme are shackled and led into the underground laboratory where they are confronted by Dr. Vindi. The unhinged genius declares that he is creating life. He stands before a shielded cabinet filled with small vials of glowing blue liquid, and announces the return of the infamous Blue Shadow Virus, a deadly plague wiped from the galaxy generations ago. Vindi has cultivated it once more. Furthermore, he has created an airborne version of the virus -- no longer is it contained only to water. Placed within bombs, the gaseous virus is now an incredibly potent weapon.
To Vindi's demented way of thinking, the eradication of the virus was tantamount to genocide. The thousands upon thousands of multicellular organisms spreading war throughout the galaxy are the real plague, and they should not be afforded any superiority.
A Republic gunship lands at Theed palace, and Obi-Wan Kenobi, Ahsoka and Anakin Skywalker emerge. They are met by Typho, who reports that Padme has gone into the swamps to investigate the outbreak. Anakin is alarmed at this news. Typho introduces Peppi Bow, the last person to have seen Padme and Jar Jar. Anakin dispatches Ahsoka to accompany Peppi in the search for Padme.
Typho briefs the Jedi; the Naboo technicians did further robolobotomies on the battle droids, uncovering a holographic image of Doctor Nuvo Vindi, Senior Medic of the Perma families who disappeared about ten years ago. The snippet of holographic recording shows Vindi plotting to release one Blue Shadow virus bomb for each star system.
Typho next reveals the result of the geo-scan of the coordinates that Padme dispatched. The sensor readings uncovered a huge underground laboratory, with three entry points and a large hangar. Radiation scans also pinpoint a likely location for the bomb assembly room.
The situation is dire -- the weaponization of Blue Shadow Virus could lead to a galaxy-wide plague. The Jedi need to strike quickly, decisively -- and accurately. A careless blast might unleash the virus on Naboo. Obi-Wan pragmatically weighs the risks -- better one planet be poisoned and the plot stopped than thousands of worlds fall victim to the virus.
In the eastern swamps, Peppi and Ahsoka ride shaak-back and find Padme's scout carrier. They spot Jar Jar and Padme's tracks in the mud. Suddenly, the periscope emerges underneath Peppi's feet. Both Ahsoka and Peppi try to stay out of the scope's field of vision.
Night has fallen. Ahsoka reports in to an edgy Anakin. There is no sign of the Senator, so Ahsoka assumes she is in the lab. However, the lab entranceways are lined with pressure sensors. There is no way to enter undetected. Obi-Wan orders AHsoka to detonate a bunker-bomb at the south end of the facility; she is cause a distraction that seals off the bomb area while Kenobi and Skywalker come in through the hatches.
A trio of gunships arrive at the hangar, ready to take the Jedi into the swamps. Kenobi will take care of the virus bombs while Anakin is to focus on the doctor. Obi-Wan reminds Anakin to focus on the mission and not be distracted by Padme.
Back in the swamps, Ahsoka levitates a bunker bomb thermal detonator charge past the periscopes and at the swamp compound's south end and detonates it. Alarms ring throughout the lab. Vindi orders all droids to hatch number one, while he dons a special breather helmet.
The gunships arrive at the swamps. Peppi wants to join in the fight, but Ahsoka tells her to stay behind and make sure no one escapes. Peppi reluctantly agrees.
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. The droids are concentrated at Ahsoka's entrance; her distraction seems to have worked. With the arrival of droidekas, Ahsoka orders her troops to fall back. Elsewhere, Dr. Vindi's assistant droid has spotted the clone attackers, and runs for it, carrying a Blue Shadow Virus bomb.
Anakin leads his troops to the laboratory, cutting through the airlock doors. He spots Padme and Jar Jar tied to an electric terminal. Dr. Vindi stands at the terminal's control, warning Skywalker that if he takes another step, the prisoners will be fried. He orders the Republic invaders to drop their weapons. Skywalker has no choice but to comply and tosses his lightsaber to the floor. The clones drop their guns, and the battle droids surround them.
The droidekas harrying Ahsoka's troops are suddenly taken out by the collapse of a tunnel caused by Obi-Wan Kenobi. He has arrived with a special bomb squad team of clone troopers.
Vindi knows he can't hold Anakin for long, so he instead craftily 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 jumps past the firing battle droids to grab his lightsaber, spins and turns and cuts them down, and then uses the Force to toss a super battle droid at the terminal controls. He checks to see if Amidala is all right. She's shaken, but will survive.
Elsewhere in the compound, Obi-Wan races to the bomb assembly area, while Ahsoka holds off the droids. He and his squad find the room filled with rows of inactive explosives. The bombs suddenly light up as Dr. Vindi remotely activates them. Kenobi surmises that Skywalker didn't capture the doctor. He also notices an empty slot amid the rows of bombs -- one of the explosives is missing.
Anakin orders Ahsoka to search for the wayward explosive. Padme remembers Dr. Vindi's assistant, and correctly guesses that it's the keeper of the missing bomb. The teams split up to find the droid.
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. Vindi raises the landing platform so he can escape in his shuttle. Anakin begins to cut through the door, and radios to Obi-Wan for help.
Padme and Jar Jar discover a room filled with a small grove of trees. Inside, Dr. Vindi's droid cowers. Padme corners it, and it makes a break for it. Jar Jar tackles the droid, dropping the bomb which Padme catches. She radios her success to Ahsoka, who dispatches the bomb squad to Padme'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, splitting the swamp floor beneath Peppi Bow's feet. Daylight streams 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 lies prostrate on the landing platform surface, cackling with glee because his timed bombs are ready to erupt. But there is no explosion.
The clone troopers have deactivated all the bombs.