Aayla Secura joined the Jedi mission to Geonosis, which became the opening battle of the Clone Wars. Aayla fought bravely, but was surrounded by Separatist forces. She and her fellow Jedi prepared to fight to the death, but were saved by the arrival of Yoda and clone troopers aboard gunships.

During the Clone Wars, Aayla served as a Jedi General, commanding a Republic task force at Quell. Her ships were devastated by a Separatist attack, with disaster averted only by the timely arrival of Anakin Skywalker, leading a task force of his own.

Aayla, Anakin and Ahsoka escaped the Battle of Quell aboard a Republic frigate, but Anakin was badly hurt during the battle. And Aayla’s clone commander, Bly, had worse news: the frigate was on a collision course with a star.

The frigate didn’t hit the star, but it crash-landed on the grassy planet Maridun. While Rex watched over Anakin, Aayla headed out with Ahsoka and Bly to search for help.

Aayla’s party discovered a village of Lurmen, who greeted the outsiders warily. The Lurmen were pacifists who’d fled the horrors of the Clone Wars, and now feared these Republic refugees had brought the war to them once again. But they agreed to tend to Anakin’s injuries.

War did indeed come to Maridun – the Separatist scientist Lok Durd chose the planet to test his defoliator weapon. Aayla and a recovered Anakin led an attack on the Separatist camp, hoping to save the Lurmen and seize a ship for transport off Maridun.

With help from some of the younger Lurmen, the Jedi and clones defeated the Separatists and destroyed Durd’s defoliator tank. They then left Maridun to rejoin the war effort.

When the Zillo Beast broke out of a scientific lab and rampaged across Coruscant, Aayla joined Yoda in coordinating the Jedi’s efforts to subdue the monstrous creature.

Aayla joined other Jedi Generals leading troops in the Outer Rim Sieges, as Republic forces pushed the Separatists to their breaking point. She listened with grave concern as Mace Windu and Yoda warned that the Jedi might have to remove Supreme Chancellor Palpatine from office and take over the Senate.

The Clone Wars had reached a crisis point. But like the other Jedi, Aayla had no idea that the galactic conflict was part of a Sith plot to rule the galaxy. After defeating Mace Windu and seducing Anakin Skywalker to the dark side of the Force, Palpatine issued Order 66 to his clone commanders. Bly relayed the order to his troops and they opened fire on Aayla, killing the Jedi General they had served alongside.