In the vicinity of 9 BBY, the Galactic Empire carried out a sterilization of the Geonosis world situated in the Outer Rim. This extermination, ordered by Grand Moff Wilhuff Tarkin, resulted in the death of the majority of the planet's inhabitants. The motive behind this horrific act was to safeguard the secrecy surrounding the Death Star project. It was the Geonosians from the Stalgasin hive who originally constructed the Death Star, a heavily armored battle station with the capability to obliterate entire planets. During the Clone Wars, Lieutenant Commander Orson Callan Krennic convinced them to contribute to the battle station's creation.
As the war concluded, Palpatine, then serving as Supreme Chancellor, proclaimed himself Emperor and transformed the Galactic Republic into the Galactic Empire. The Death Star project then became an Imperial asset, and the battle station was relocated from Geonosis. The lone survivor of the sterilization was Klik-Klak, who later acquired a Geonosian egg from which Queen Karina hatched. Karina eventually established her lair deep beneath the planet's surface. Unable to reproduce and replenish her species, Karina continued the production of battle droids in the same Geonosian droid factories that had operated before. During the Galactic Civil War, the Sith Lord Darth Vader arrived on Geonosis and seized these droids from her.
In the time leading up to the Clone Wars, the Geonosians conceived an Ultimate Weapon for the Confederacy of Independent Systems. This weapon, which would later become known as the Death Star, was a fortified armored battle station with the power to annihilate entire planets. When the Clone Wars erupted on their homeworld of Geonosis, Count Dooku, a Sith Lord and leader of the Separatist Alliance, took the designs for the Ultimate Weapon to his master, Darth Sidious, on Coruscant. Sidious was secretly Supreme Chancellor Palpatine, who was in charge of the Galactic Republic and controlled both sides of the war. His objective was to transform the Republic into a Galactic Empire and govern the galaxy as Emperor.
Sidious' ambitions were realized at the conclusion of the Clone Wars. The Separatists suffered defeat, and the Republic was restructured into the Empire. The Death Star project continued its development above Geonosis, initially under the direction of Vice Admiral Dodd Rancit, and subsequently under Moff Wilhuff Tarkin. After the existence and location of the Death Star above Geonosis became known throughout the galaxy, Tarkin, now holding the rank of Grand Moff, ordered the station to be relocated to maintain secrecy. Eventually, the station was moved to the remote world of Scarif. Following the Death Star's arrival on Scarif, Tarkin instructed the Imperial Weapons division to sterilize Geonosis in order to eliminate any potential leaks of information about the super weapon. Under Tarkin's command, the Imperials deployed Imperial gas canisters containing toxic insecticide. This assault decimated nearly the entire planet's population of approximately 100 billion, marking the most extensive act of genocide perpetrated by the Empire.
Within a few months of the genocide, the Death Star project was fully operational above Scarif. In 3 BBY, three years prior to the Battle of Yavin, the rebel crew of the starship Ghost journeyed to Geonosis after receiving intelligence suggesting Imperial activity there.
Upon arrival, they discovered only Imperial construction modules that had previously supported the Death Star's construction, though the rebels did not know what had been built there. The intelligence was actually a trap to lure the rebels to Geonosis. Agent Kallus of the Imperial Security Bureau led a group of stormtroopers in an ambush against the rebels on one of the modules, but the rebels managed to escape. Garazeb Orrelios, one of the rebels, became stranded with Agent Kallus on Bahryn, an icy moon of Geonosis, after their escape pod crashed. Before their rescue, Orrelios learned that Kallus was unaware of the events on Geonosis. Kallus refused to believe that the Empire would exterminate an entire population without reason, but Orrelios accused him of being in denial.
The following year, Senator Bail Organa sent Saw Gerrera and his Partisans to investigate the apparent disappearance of the Geonosian species. Saw and his team were ambushed and attacked by Klik-Klak, who mistook them for enemies. After Rebel Command lost contact with Saw and his team, Senator Organa dispatched the Spectres and the former Clone Captain Rex to continue Saw's mission. After reuniting with Saw, the Spectres and Rex captured Klik-Klak. A disagreement arose between Saw, who wanted to take Klik-Klak offworld for interrogation, and the Spectres, who wanted him to remain on Geonosis.
The rebels were forced to take their ship Ghost into the depths of Geonosis after they were attacked by a light cruiser commanded by Captain Brunson. Down there, the rebels discovered the poison canisters which the Empire had used to perpetrate genocide against the Geonosians. The rebels managed to flee Captain Brunson's cruiser but were unable to bring back physical evidence of the poison canisters. However, the rebellion was able to use visual images of the canisters to rally more worlds to the rebel cause.
Years later, during the Galactic Civil War, the Sith Lord Darth Vader and the archaeologist Doctor Aphra embarked on a secret mission to Geonosis to acquire battle droids for his personal army. They located Karina, who was still producing battle droids in the same Geonosian droid factories that had operated before and during the Clone Wars. Vader seized her battle droids but spared the queen's life. Mon Mothma, the rebel leader, indirectly referenced the Geonosian genocide in her Declaration of Rebellion, condemning the Galactic Empire for its "blatant policy" of speciesism and genocide against the galaxy's non-human populations.