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Nute Gunray was the Viceroy of the Trade Federation and a Neimoidian. He was involved the famous Invasion of Naboo at the behest of his myterious benefactor Darth Sidious. As soon as the Clone Wars started, Gunray pledged his support to the Confederacy of Independent Systems, while Lott Dod denied that the Trade Federation had any connections to the Separatists.
At some point following the Battle of Geonosis, Nute Gunray turned his attention to the Mid Rim world of Rodia. The planet had been attacked by pirates and Rodia's Republic Senator Onaconda Farr had appealed to Viceroy Gunray for help. The Viceroy agreed to send relief supplies to Rodia in return for one small favor: kidnapping his long-time foe Senator Amidala. Farr was a close friend of the Naboo Senator and called her to Rodia under the pretext of seeking aid from the Republic for the Rodian people. Senator Padmé Amidala was escorted by her long-time friend Representative Jar Jar Binks and her protocol droid C-3PO.
Upon arriving, Senator Amidala and C-3PO were captured. After learning of her capture, Gunray ordered that she be manacled as a precaution before he traveled to Rodia to meet her. However, Gunray's plans encountered an unexpected obstacle in the form of Binks, who managed to elude the Viceroy's battle droids and trick them into believing that he was a Jedi. In the midst of the commotion, Amidala and C-3PO managed to escape and contact the Republic for assistance before they were recaptured by Gunray's battle droids. After arriving on Rodia, Gunray applied pressure on Senator Farr by withholding relief supplies until Senator Amidala was executed. When Senator Farr protested, Gunray responded that the planet was now under his protection.
After Gunray's droid forces had recaptured Senator Amidala and C-3PO, he assembled a trio of droidekas to execute them. Before Gunray could carry out the sentence, Binks and a Kwazel Maw monster that he had befriended named "Bogey" burst out from the swamp and overwhelmed the droidekas. The Viceroy attempted to flee aboard his Sheathipede-class transport shuttle but "Bogie" knocked it into the swamp. He was then held by Senator Amidala at gunpoint. Shortly later, Senator Farr arrived and revealed that he and Senator Amidala had planned to trap Gunray all along. Shortly later, Republic forces of the 41st Elite Corps arrived and took Gunray into custody.
Cloak of Darkness
Following the events on Rodia, the captive Viceroy Gunray was transferred aboard the Venator-class Star Destroyer Tranquility for trial on Coruscant. Due to his high status in the Confederacy, the Jedi Council dispatched the Jedi Master Luminara Unduli and Anakin Skywalker's Padawan Ahsoka Tano to guard Gunray. The two Jedi were reinforced by a group of Senate Guards led by Captain Faro Argyus and a squad of Clone troopers led by Clone Commander Gree. In response to Gunray's capture, Darth Sidious and his apprentice Count Dooku dispatched the Dathomirian dark side assassin Asajj Ventress to infiltrate the Tranquility and rescue or kill the Trade Federation Viceroy.
While in captivity, Gunray was interrogated by Unduli and Tano but refused to cooperate. When a frustrated Tano threatened the Viceroy, Master Unduli chastised the younger Jedi. Their interrogation was interrupted by the arrival of Separatist attack force consisting of Separatist Vulture droids and three Droch-class boarding ships. While Separatist droids boarded the Tranquility, Ventress took advantage of the chaos to sabotage the ship's power generators. After Unduli departed with several Clone troopers to fight the intruders, Ventress managed to overpower Ahsoka and free Gunray. Before Gunray could escape with the dark side warrior, Master Luminara returned to the cell and fought with Ventress in the ship's elevator shaft and generator room.
While Luminara was dueling with Ventress, Gunray was locked in his cell with Tano and Captain Argyus standing guard. Unknown to the Republic and Jedi, Argyus was a traitor who was secretly working for Count Dooku. When Ahsoka departed the brig to help Luminara, Argyus took the opportunity to overpower his fellow commandos and free Gunray. Commander Gree managed to overpower Argyus but was knocked in the head by Gunray. The Viceroy and his rescuer then escaped on a Republic Consular-class cruiser in the lower hangar and were joined by Ventress, who had escaped her Jedi foes in a Republic escape pod. Gunray was present when Ventress killed Argyus by impaling him through the chest with lightsaber, and after the death Gunray told Ventress he had "always had a good feeling about" her, which was what he had told Argyus as well.
Lair of Grievous
Following his escape, Nute Gunray assisted Count Dooku to lure Jedi Master Kit Fisto, and Jedi Knight Nahdar Vebb, and several clone troopers into a trap at General Grievous's fortress on Vassek. Count Dooku wanted General Grievous to prove his worth by killing the intruders. As part of the plot, a hologram of Gunray was used to taunt his Jedi and Republic pursuers. Shortly later, the Jedi and Clone troopers were attacked by Grievous. Nahdar Vebb and all the Republic clones present on the mission, with the exception of Fisto, were killed.