One of the wealthiest corporate organizations in the galaxy, the Trade Federation controlled most of the interstellar shipping passing through the Rim territories. The Trade Federation was headed by Viceroy Nute Gunray, and even had its own representative in the Republic Senate to lobby for even greater power. On the orders of Darth Sidious, the Trade Federation sent its battle droids to invade Naboo to create a government crisis. During the Clone Wars, the Trade Federation secretly signed on as a member of Count Dooku's Separatist organization, though representatives in the Senate tried to deny this.
Neimoidians are known for their business skills, but Nute Gunray, Viceroy of the Trade Federation, was more cutthroat than most. It was Gunray who conspired with the Sith Lord Darth Sidious to launch the blockade and subsequent invasion of Naboo. Once the planet was under siege, Gunray attempted to force Queen Amidala to sign a treaty that would legitimize the occupation. Amidala escaped, and returned to infiltrate her own palace and blast through Gunray's protectors. Arrested by Republic officials, Gunray was carted off to answer for his crimes, but evaded imprisonment and kept his post.
To hear Lott Dod tell it, the actions of Nute Gunray did not reflect the true intents of the Trade Federation, which remained loyal to the Galactic Republic. Sure, the Separatist Alliance did use Trade Federation starships and battle droids as part of their fighting forces in the Clone Wars, but this was equipment legitimately purchased in the open market. The Trade Federation was committed to commerce across the entire galaxy, and had no interest in getting caught up in territorial wars, Dodd would say. In truth, the Senator received a healthy income to ensure both sides of the war stay well equipped.
A cowardly Neimoidian official, Rune Haako had no shortage of despair during the Trade Federation blockade and invasion of Naboo. As lieutenant to Viceroy Nute Gunray, Haako was privy to his superior's plans and knew of the mysterious Sith patron who was the true mastermind behind their bold maneuvers. Haako, when beyond Sith earshot, openly questioned Gunray's judgment in striking this terrifying alliance. When Queen Amidala retook her capital of Theed, Haako and Gunray were captured and sent to Coruscant for trial and punishment.
The Confederacy of Independent Systems, also known as the Separatist Alliance, was a collection of star systems and corporate titans that left the Republic and fought for independence against the Republic’s clone armies and Jedi Knights. The charismatic former Jedi Count Dooku was the Alliance’s political leader, while its military power came from credits and assets donated by powerful galactic trade groups. No one suspected that the Alliance was actually a tool of Darth Sidious, who had engineered the Clone Wars as part of a Sith plot to rule the galaxy.