Several years before the Clone Wars began, Organa was contacted by a group dubbed the Friends of the Republic as he served as the head of negotiations between Alderaan and Chandrila to settle a joint mining venture. The group gave him the information needed to thwart an unspecified diplomatic and humanitarian disaster that Organa believed would engulf much of the Galactic Republic. He kept in contact with the Friends of the Republic thereafter, receiving occasional bits of intelligence regarding the war. In 22 BBY, the group contacted him on a secret comlink, granting him information regarding a society of beings who utilized the dark side of the Force called Sith who were planning an assault on the Jedi Order. Organa immediately took the information to his friend Senator Padmé Amidala, who had undertaken matters on behalf of the Jedi before and whom he considered an honorary Jedi herself. After relating the information to her, Amidala made a call to the Jedi Temple, asking Obi-Wan Kenobi to meet at her apartment, where Organa related the tale to him, much to the Jedi Master's skepticism. The meeting adjourned shortly afterward, with Kenobi promising to keep an open mind and to watch out for any potential threats. Days later, Organa received another communique from the Friends, this time bestowing him with the specific location of a Sith temple on Zigoola. The Senator bypassed Amidala this time, contacting Kenobi at the Jedi Temple directly and meeting at Organa's apartment, where he informed his Jedi confidante that he had initial coordinates and would be making the trip to Zigoola with or without Jedi assistance. Unwilling to allow a politician so inexperienced in combat take on such a vital mission alone, Kenobi contacted the Temple and was granted permission to accompany Organa on his quest.
The mission took place in several stages, starting out as Organa's private vessel cleared Coruscant's airspace, triggering a pre-recorded away message that let the Friends know he was ready to upload coordinates. The first stretch led the two to space bordering Kuat, then from there to Atzerri. Though the men initially took a disliking to each other, they were able to pass the time with games of sabacc and philosophical debates, Kenobi meditating intermittently and Organa working on political business for the Senate. While waiting for their next set of coordinates at Atzerri, Kenobi began suffering vivid nightmares during his meditations, but shook them off as the Friends instructed them to continue on to Munto Codru, in the distant reaches of the Outer Rim.
The coordinates by Munto Codru revealed only one landmark: a decrepit space station, which the two traveling companions decide is the headquarters of the Friends of the Republic. Pushing Organa's vessel into the docking bay, it became more and more evident that a struggle had taken place recently, and through examination of the discarded weapons and several bodies, Kenobi was able to deduce that the station had been attacked by pirates. Moving swiftly through the station, the two came to the command center, where they found one woman fighting off the rest of the attackers and their assault droids. Largely through use of the Force and a lightsaber, the Kalarba pirates were defeated and the woman was able to reveal herself as Alinta, Organa's contact. As it became more and more obvious that Alinta had suffered a mortal wound, she made it a point to give the men the final coordinates they needed to reach Zigoola. She died shortly thereafter, giving them her final instructions to destroy the space station as they leave. Although Organa was initially hesitant, Kenobi upheld his pledge and the Friends of the Republic were obliterated into space.
Alinta's final coordinates led the two into Wild Space, where they did indeed come across the Sith planet. With just a bit of trepidation, Kenobi attempted to land the ship, only to find himself overwhelmed by a Sith presence in his mind compelling him to Force choke Organa and crash the yacht. While the Jedi Master was able to break free of the hold just in time, he was unable to prevent their only mode of transportation from crashing into the planet's surface. Reawakening later and holding a brief firelight conference with his traveling companion, Kenobi came to the conclusion that the only possible way to survive would be to reach the Sith temple and use one of the artifacts to make contact with a Jedi at the Temple. Having spotted their goal during the crash landing, Kenobi and Organa begin their trek, suffering days of pounding Sith mental attacks; several complete breakdowns including one in a forest which led to a scathing lightsaber assault against the hallucination of Asajj Ventress darting through trees; and several recursions back into haunting memories such as firebeetles, the deaths of Tayvor Mandirly, Xanatos and Qui-Gon Jinn and his and Anakin Skywalker's mutilation at the hands of Count Dooku during the Battle of Geonosis. Through pounding rain and lightning storms, Kenobi and Organa clambered through to the temple, utilizing Kenobi's discovery that pain dulled the Sith voices and instructing Organa to use his lightsaber whenever necessary. Although they reached the temple in more or less one piece, Kenobi collapsed just outside and Organa was forced to go in on his own, despite having absolutely no clue what any of the artifacts did. Realizing this fact, the Senator crawled outside and forced Kenobi to accompany him, tortuously finding a crystal that enhanced long-distance Force communication.
Deep in meditation on Coruscant, Grand Master Yoda sensed Kenobi's call, as well as a massively strong dark side presence that would prove a mortal danger to any Jedi sent to rescue him. He made a personal call to Padmé Amidala, asking her to undertake the mission to Zigoola with Captain Korbel. Amidala accepted, and made the mission unmolested, successfully picking up Kenobi and Organa and transporting them back to Coruscant.
Due to Kenobi's tampering with the artifacts and triggering security measures in the Sith temple, the building collapsed in on itself, destroying its dark power and all of the dark side weapons within. Although both Kenobi and Organa were gravely injured and exhausted from the mission, they were able to complete their objective and form a lasting friendship, which would result in Kenobi trusting Organa as the adoptive father of Anakin Skywalker and Padmé Amidala's daughter Leia Organa Solo.