Nute Gunray was a Neimoidian from the planet Neimoidia. Following a stint as Minister for the Trade Federation, he rose in power after the Stark Hyperspace War in 44 BBY, eventually becoming Viceroy of the Trade Federation. In 32 BBY, Gunray participated in the occupation of Naboo to settle a trade dispute that began in the Galactic Senate. With the help of Darth Sidious, Gunray invaded the planet to end the trade dispute and secured all facilities in the capital of Theed. He attempted to force the incumbent Queen of Naboo Padmé Amidala to sign a treaty to make the invasion of his legal, however she denied and the Siege of Naboo continued. The Trade Federtion soon surrendered to Naboo forces following the Second Battle of Theed. Gunray was taken to the Galactic Republic captial on Coruscant to be charged with acts of war.

During the ten years following the Invasion of Naboo, Gunray confronted former Jedi Master, Count Dooku, who began a separatist movement that opposed the Republic. Dooku, who secretly was Sidious's Sith apprentice under the name of Darth Traynus, helped the Viceroy through his four trials in the Supreme Court, and soon after the trials, Gunray retained his position as Viceroy. The Trade Federation, under Gunray's command, joined Dooku's separatist movement and he was named Leader of the Separatist Council. Gunray, along with Dooku and his master, Sidious, formed the Confederacy of Independent Systems which opposed the Galactic Republic in a three year war known as the Clone Wars.

During the Clone Wars, Gunray was called to the swamp planet of Rodia where he helped the people on Rodia from pirate attackers. However unbeknownst to Gunray, Senator Amidala, the former Queen of Naboo, was on Rodia at the time. Gunray was betrayed after the Rodian forces gave the Viceroy to Amidala. Gunray was given to Jedi Master Luminara Unduli and Jedi Padawan Ahsoka Tano. Dooku sent his Dark Jedi apprentice, Asajj Ventress, to rescue the Viceroy from the Republic forces. Stationed inside the Republic star destroyer, Senate Commando Argyus released the Viceroy and met up with Ventress in Argyus's cruiser. Though, Argyus was killed by Ventress who told her that he will tell Dooku of his success in the rescue of Gunray.

In 19 BBY, the Separatist Council was moved to the volcanic planet of Mustafar, after Confederate General Grievous became leader of the CIS after the death of Dooku. Gunray along with the other Separatist leaders were betrayed by Darth Sidious after he sent his new apprentice, Darth Vader, to Mustafar to end the War. Gunray was the last council member to be killed by Vader's lightsaber.