The Geonosis investigation mission, alternatively known as the Geonosis mission, was an operation led by Partisan leader Saw Gerrera in 2 BBY. Gerrera journeyed to the desert planet Geonosis, seeking to uncover the nature of a large-scale construction project previously established by the Galactic Empire within the Geonosis system. A deflector shield generator lured him and his team into a subterranean maze. This labyrinth was home to Klik-Klak, the lone survivor of the Sterilization of Geonosis. Klik-Klak, perceiving Saw and his group as a threat, killed most of them, sparing only Saw.
Subsequently, Senator Bail Organa and Commander Jun Sato dispatched the Spectres along with Captain Rex to Geonosis. Their mission was to locate Saw and investigate the apparent extinction of the Geonosian species. Rex, Kanan Jarrus, Ezra Bridger, and Chopper encountered Saw and, after a lengthy chase, aided in capturing Klik-Klak. Meanwhile, Sabine Wren and Garazeb Orrelios discovered a deflector core. Following intense debate, Ezra and his fellow rebels successfully persuaded Saw to allow Klik-Klak and the last Geonosian Queen egg to remain on the planet.
The arrival of an Arquitens-class command cruiser under the command of Captain Brunson complicated the mission. After a short aerial engagement with TIE bombers, the Ghost sought refuge in a vast air shaft that descended into Geonosis's depths. The rebels and Saw united to fend off Imperial Jumptroopers. While returning Klik-Klak and the Geonosian Queen's egg, the rebels and Saw came across poison canisters, revealing the Empire's method of exterminating the Geonosians. They then narrowly escaped the air shaft before Brunson's light cruiser could bury them under rubble. The rebels carried news of the Geonosian genocide and a new deflector core back to the rebellion.
After the conclusion of the Clone Wars, the Galactic Empire initiated an ambitious endeavor to construct a superweapon that would later be known as the Death Star. The Empire coerced numerous Geonosian weapons engineers to assist in the Death Star's development. When the Geonosians failed to create a functional superlaser, Imperial Director Orson Krennic recruited Galen Erso to finalize the project. Once the work crew had developed a working hyperdrive, the Empire bombed and sterilized the planet Geonosis and eliminated its population to maintain the superweapon's secrecy.
In 2 BBY, Rebel Command tasked the rebel operative Saw Gerrera and his Partisans with a mission to investigate the apparent disappearance of the Geonosian species. Saw and his Partisan comrades traveled to Geonosis, reporting an energy signature before communications with Rebel Command were lost. This energy signature was revealed to be a deflector shield generator operated by Klik-Klak, the only Geonosian to survive the Imperial genocide. He resided in an underground labyrinth near a large air shaft and served as the guardian of a Geonosian Queen's egg. Klik-Klak also commanded a force of reactivated battle droids.
Klik-Klak, perceiving Saw and his team as hostile, attacked them, wiping out Saw's team with the exception of Saw himself. In desperation, Rebel Command sought assistance from Senator Bail Organa and Commander Jun Sato to dispatch the Spectres and Rex to Geonosis. Their objectives were to find Saw's team and retrieve any data he had uncovered. The Spectres, led by Phoenix Leader Hera Syndulla, were part of a rebel cell known as the Phoenix Cell. Hera's crew had previously visited Geonosis and engaged in a skirmish with Imperial forces at an Imperial construction module.
Despite the presence of a sandstorm, the Spectres' ship, the Ghost, successfully landed on Geonosis near the source of the energy reading. Under Hera's direction, Rex, Kanan Jarrus, Ezra Bridger, and Chopper ventured into a Geonosian structure that marked the last known location of Saw's transmission. The rebels infiltrated a hole leading into an underground labyrinth. Discovering abandoned rebel equipment, they resolved to locate Saw, prompted by Rex's determination not to abandon a former comrade. Reaching a dead end, the rebels were ambushed by several old Clone Wars-era B1-series battle droids and a droideka. A brief battle erupted, with Saw destroying the droids with a skirmish. Kanan and Ezra used their lightsabers to destroy the droideka.
Saw informed the rebels of his team's discovery of an operational shield generator. He explained that his squad had been attacked and eliminated by a Geonosian. Believing that the Geonosian possessed information regarding the Empire's extermination of Geonosis's population, Saw persuaded Kanan and Ezra's team to assist him in finding the Geonosian. After the rebels and Saw reached a large air shaft leading to the surface, Kanan successfully re-established contact with the Ghost. Kanan warned Hera about the presence of operational battle droids on Geonosis.
Concurrently, Hera had dispatched Sabine Wren and Garazeb Orrelios to investigate the source of the energy reading, which proved to be an operational shield generator. Under Hera's command, Sabine and Zeb began extracting the deflector core. Before they could return to the Ghost, the two rebels discovered that the generator was surrounded by several deactivated droidekas. Following Hera's warnings, Sabine and Zeb decided to transport the deflector core back to the Ghost.
After Chopper illuminated the opposite side of the air shaft with a searchlight, the rebels and Saw spotted a hidden Geonosian. The Geonosian used a remote controller to activate the droidekas guarding the deflector shield generator before fleeing further into the labyrinth. Unable to cross the shaft, Kanan used the Force to safely propel Ezra to the other side. Chopper activated his rocket boosters and joined the pursuit. Kanan then used the Force to lower a bridge above, allowing Saw and Rex to cross as well. Once everyone had crossed, Kanan Force-leaped to the other side.
Meanwhile, Sabine and Zeb found themselves under attack from the droidekas. Sabine managed to activate the deflector core, creating a deflector shield that absorbed the droid's blaster fire. Back at the labyrinth, the Spectres and Saw successfully captured the lone Geonosian after a prolonged chase. Saw also managed to shoot the Geonosian's droid controller, deactivating the droidekas attacking Sabine and Zeb. Saw then demanded that their Geonosian captive reveal what the Empire was constructing above Geonosis.
While Saw aggressively interrogated the Geonosian captive, Ezra attempted to convince him that they were not hostile. Ezra's kindness resonated with the Geonosian, who identified himself as Klik-Klak. Unable to speak Galactic Basic Standard, Klik-Klak attempted to communicate by drawing two circles on the ground. While Saw did not understand the Geonosian's message, Ezra recalled that Chopper had detected an energy reading earlier. Although Ezra's team was willing to trust Klik-Klak, Saw harbored resentment towards the Geonosian species due to their support for the Separatists during the Clone Wars.
A restrained Klik-Klak led the rebels and Saw to his dwelling, which served as both a workshop and a generator for maintaining his battle droids. Inside, the rebels also discovered an operational transmitter, which they used to reestablish contact with Hera and arrange a rendezvous at the central air shaft. Ezra learned that Klik-Klak was the custodian of the last Geonosian Queen's egg. While Saw wanted to take Klik-Klak back for interrogation, Ezra insisted that Klik-Klak belonged with his people. As a compromise, Kanan managed to persuade Saw to allow them to take Klik-Klak to Chopper Base for interrogation and then safely return him to Geonosis.
The Spectres' mission on Geonosis was complicated by the arrival of an Arquitens-class command cruiser under the command of Captain Brunson. Brunson's ship was responding to a proximity alert triggered by the rebels' presence. Brunson deployed two recon TIE bombers, which encountered the Ghost. By that point, the rebels had safely stored away their deflector core, and Zeb had returned to the ship after successfully connecting Kanan and Hera's signals. Sabine and Zeb used the Ghost's laser cannons to shoot down the Imperial bombers.
Hera skillfully piloted the Ghost into the air shaft and rendezvoused with Kanan's team, Saw, and Klik-Klak. Once aboard, a disagreement arose between the Spectres and Saw regarding the treatment of Klik-Klak. Saw wanted to depart immediately with Klik-Klak on the Phantom II. When he tortured Klik-Klak with an electro-transmitter, Ezra, Rex, and the others protested Saw's harsh methods. Desperate, Saw threatened to shoot the Geonosian queen's egg to obtain results. Rex and Ezra managed to reason with Saw, warning him that resorting to such violence would make him no better than his Imperial adversaries.
Saw and his rebel allies set aside their differences when Captain Brunson's light cruiser arrived over the central air shaft, blocking their escape. Brunson deployed a squad of Jumptroopers to board the Ghost. Ezra, Kanan, Rex, Zeb, Saw, and Sabine successfully repelled the boarders after a brief battle. Sabine even used her jetpack to sneak up behind two Jumptroopers and kill them with grenades. The Ghost then descended into the depths of Geonosis.
Upon reaching the bottom, the rebels and Saw discovered several poison canisters that the Empire had used during the Sterilization of Geonosis. Having discovered irrefutable evidence that the Empire had perpetrated genocide against the Geonosians, Saw freed Klik-Klak, allowing him to retreat deeper underground with the Geonosian queen egg. Despite his past animosity towards the Geonosians, Saw realized that they deserved the same opportunity to rebuild as everyone else. After collecting a few canisters as evidence, the rebels decided to flee Geonosis.
By that stage, Captain Brunson had ordered her crew to bury the rebels alive by collapsing the air shaft on top of them. The crew of the Ghost managed to blast their way out by firing proton torpedoes, which ignited the Imperial light cruiser. They then managed to slip through the burning vessel. Captain Brunson survived the inferno but was humiliated by the rebels' successful escape. However, the rebels dropped the poison canisters, losing their physical evidence of the Imperial genocide.
As a consequence of the mission to Geonosis, the Spectres and Saw Gerrera uncovered the Empire's genocide against the Geonosians. Despite taking photos of the canisters, Senator Organa informed them that these images would be insufficient to sway the Imperial Senate against the Empire. However, he assured them that it would persuade more worlds to join the rebellion. Despite this setback, Commander Sato reassured the Spectres that their mission was a success because they had rescued Saw and obtained a deflector core. In addition, the crew of the Ghost also helped ensure the survival of the Geonosian species by helping Klik-Klak to escape with the Geonosian queen's egg into the depths of Geonosis. Despite their partnership with Saw, the Spectres remained uneasy with Saw's methods.
Later, the Alliance to Restore the Republic's Declaration of Rebellion condemned the Empire for instituting speciesism and genocide against alien species.
The mission to Geonosis was initially mentioned in the 2016 reference book Star Wars: Rogue One: The Ultimate Visual Guide. It subsequently became the focus of the Star Wars Rebels double episode "Ghosts of Geonosis," which premiered on Disney XD on January 7, 2017.