The Great Aquilaris Deluge unfolded during the Second Charge Matrica's campaign on Aquilaris, specifically in 1032 BBY. Zodoh, a Hutt crime lord, successfully demonstrated the power of his Stormdriver superweapons on the planet Aquilaris. These Stormdrivers, massive capital ships, employed moisture vaporators to create immense, artificial floods across Aquilaris, resulting in numerous civilian deaths and widespread destruction of infrastructure. Amidst this catastrophic flooding, Jedi Knight Kerra Holt, in collaboration with the Seacroppers, heroically rescued thousands by evacuating survivors to underwater harvester stations.
Captain Kerra Holt of Devil Squadron intervened to halt the Stormdrivers' global flood. She triggered a series of explosions and made her escape from Zodoh's flagship, the Voracious. This intervention disrupted the coordinated flooding, leading to a gradual recession of the waters.
Despite this interference, Zodoh considered the Deluge a success. It validated the effectiveness of his Stormdrivers, and he saw Aquilaris as a potential source of seafood to exploit. With his objectives met, Zodoh initiated an assault on Darkknell, the capital of Sith Lord Daiman's realm.
Following the capture of Devil Squadron, Aquilaris Minor was left with almost no defenses. This situation was ideal for the Hutt crimelord Zodoh, who intended to position his Stormdriver fleet around the planet. These ships would then use their moisture vaporators to generate a planet-wide flood. Zodoh's ambitions included overthrowing the Sith warlords within the Grumani sector and establishing his own empire. He also sought to seize Grace Command's supply of Deluge spice and produce his own version of the addictive substance. This would weaken the Grumani sector's inhabitants and make them more susceptible to his rule. Zodoh pressured Captain Jenn Devaad of Devil Squadron to acquire the remaining Deluge spice by promising to free her crew if she cooperated.
Aquilaris, a world largely covered by oceans, featured low-lying continents and islands, lacking significant mountain ranges. This made its landmass extremely vulnerable to widespread flooding. The planet was poorly equipped to handle such a massive environmental disaster, as the Aquilarian people had been impoverished by the Sith occupation following the conquest of the planet in 1032 BBY. The Aquilarians lacked the necessary resources for evacuation or safe havens to accommodate refugees during the flood. The few remaining Aquilarian landspeeders were unusable in the severe storms, and boats were nonexistent, having been destroyed by the Sith Lords to prevent civilian escapes. While the Seacroppers' Guild still possessed a fleet of submersibles, they were in poor condition due to lack of maintenance. This logistical nightmare was compounded by the widespread drug addiction among the population, a result of Operation Deluge, a covert operation by the Galactic Republic's Grace Command intended to undermine the Sith war effort.

Jedi Knight Kerra Holt was the only survivor of Devil Squadron's disastrous mission. Upon returning to Capital Cay's spaceport in her Fire Lotus-class starfighter, she immediately began organizing evacuation efforts. During a meeting with the residents, Kerra encountered widespread discouragement and a significant logistical challenge. When she inquired about the potential role of the Seacroppers, a pessimistic Padgett explained that they were still addicted to Deluge spice and unable to assist, consumed only by their craving for the drug. Kerra expressed surprise that the effects of the drug persisted despite the supposed medical treatment provided by Grace Command. She inquired about using the submersibles for evacuation, but Padgett dismissed the idea, emphasizing their dilapidated state. Despite her frustrations, Kerra remained determined to proceed with the evacuation, ordering civilians to forcibly remove the Seacroppers from their barracks if necessary.
As the Aquilarian civilians began their evacuation efforts, Kerra inspected the submersibles at the docks of Capital Cay. She expressed her frustration with the growing logistical problems and the apathy of the Aquilarian civilians. While inspecting a submersible, she found a despondent and drug-addicted Joad inside the command deck. After a brief conversation about their childhood and their separation during the invasion of Aquilaris ten years prior, she attempted to persuade him to help repair the submersible for evacuation efforts. Still grieving the loss of his family, Joad refused, claiming he had nothing to live for but his Deluge addiction.
After Joad exited the command deck, Kerra, in exasperation, kicked open one of the orange food containers provided by Grace Command. She discovered it contained only Deluge spice. She quickly realized that Grace Command's relief operations were a front for distributing Deluge spice to civilian populations in Sith-occupied space. She returned to the barracks to find Captain Jenn loading spice into a shuttle and threatening the local civilians at gunpoint. Using her Force abilities, Kerra subdued Jenn and confronted her about Grace Command's spice smuggling. Joad revealed that Grace Command was a covert operation established by Baron Lemayne of Alderaan to sabotage the Sith war effort, dismissing the addicted civilians as acceptable losses in the larger conflict against the Sith.
Jenn also revealed that her animosity toward civilians stemmed from the disastrous Daalang campaign. The civilians had refused to shelter her and her Republic Navy comrades, leading to their capture and enslavement by the Hutt crimelord Zodoh. Finally, she confessed that she was trying to save her crew by acquiring the remaining Deluge stocks in Capital Cay. Kerra failed to convince Jenn to help with the evacuations. After Jenn departed in a transport shuttle, the orbiting Stormdriver fleet activated their vaporators, trapping moisture in the atmosphere and using the energy to create massive storms and floods.

Within hours, large portions of Aquilaris were submerged in torrential rain and floodwaters. Much of Capital Cay was swept away, and many civilians were trapped or killed. Kerra, along with a group of Aquilarian civilians including Padgett, began a desperate effort to evacuate civilians to Tarrah Hill, the planet's highest point. During the storm, Kerra used the Force to lift drowning civilians from the floodwaters. While on top of a submersible, she encountered Joad, who expressed remorse for his earlier animosity. As a sign of his desire to overcome his Deluge addiction, he threw his remaining stash into the floodwaters. However, Joad then surprised Kerra by diving into the flood, seemingly to retrieve his spice. In reality, he had swum under the submersible to restart its motor.
Kerra was forced to continue alone with her refugee followers to Tarrah Hill. By then, the mountain was being submerged. To the surprise of Kerra and the Aquilarian refugees, the orbiting Stormdriver ships began deactivating, ending the torrential rain. It was later discovered that Jenn Devaad had triggered a series of explosions aboard Zodoh's flagship Voracious during an escape attempt, disrupting the coordination of the Stormdriver fleet. Because the Stormdrivers were controlled by a large data-processing center aboard the fighter carrier, they were unable to continue their operations. Shortly afterward, a submersible piloted by Joad surfaced near Tarrah Hill. Kerra was relieved by her friend's change of heart, who explained that he remembered how to operate his submersibles and wanted to prove himself.
They evacuated Kerra's company of refugees to a harvester station on the ocean floor. With thousands of other flood refugees still in the flood zone, the submarine would make multiple trips to save more lives. As part of the evacuation, Kerra would lead more refugee parties to the rendezvous point at Tarrah Hill. Joad would then pilot the submarine, transporting refugees to and from the harvesting station. Meanwhile, Padgett and a group of Seacroppers began opening the sea tunnels at the harvesting station to accommodate the incoming refugees. Through these efforts, thousands of Aquilarian lives were saved.

The next day, Joad's submersible was traveling through a submerged gorge when they encountered a Hutt starfighter. Assuming Zodoh had sent starfighters to eliminate the survivors, Kerra ordered the submersible to submerge while she stood on the conning tower to confront the unidentified starfighter. Kerra quickly realized that the starfighter was flown by her former ally, Jenn Devaad, who had escaped from Zodoh's flagship Voracious. She revealed the fate of her crew and informed Kerra that Zodoh intended to attack Darkknell, the heavily populated capital of Sith Lord Daiman. Holt agreed to reconcile with Devaad, but insisted on doing things her way. The two women then departed on the Hutt starfighter for Darkknell, where they single-handedly defeated Zodoh, destroying his flagship and scattering his fleet at the last moment.
Meanwhile, the floodwaters on Aquilaris quickly receded, allowing the surviving population to return to their homes and begin the cleanup. Following the Battle of Darkknell, Devaad and Holt devised a plan to sabotage Operation Deluge. Devaad would return to Grace Command and falsely claim that she had succeeded in distributing the Deluge on Aquilaris. This would ensure that Grace Command continued to send transport ships, which Devaad would use to travel to and from Sith-occupied worlds. En route, she would dispose of the Deluge while returning to the Republic with civilian refugees. With the hidden undersea facilities on Aquilaris, the world could become a hub for transporting refugees from Sith-occupied space to safety in the Republic. As a gesture of reconciliation, Devaad allowed Holt to keep her Fire Lotus for future operations against the Sith.
The Great Aquilaris Deluge was conceived as a key plot point within the Deluge story arc of the Star Wars: Knight Errant comic series. It made its debut in Knight Errant: Deluge 3, which was released on November 16, 2011. The plot was developed by John Jackson Miller, a frequent contributor to Star Wars projects.