After Secura was promoted to the level of Jedi Knight, the Clone Wars broke out, and she was one of many Jedi to participate in the First Battle of Geonosis. She served in various campaigns, surviving such infamous battles as those on Hypori and Kamino. Indeed, such were her achievements that Secura was promoted to the level of Jedi Master near the beginning of the conflict.
As a Jedi Master, Aayla Secura led the Republic war efforts at Quell and was instrumental in the defense of Kamino and later Maridun. However, despite her undoubted prowess, Secura met her end during the instigation of Order 66 on Felucia. Master Secura was remembered for generations by the people of the worlds she had helped during her life, and stories of her were known to have become part of the culture of many such people.
Battle of Maridun
After a treacherous trip through hyperspace, the Jedi and the few clones in their company crash landed on the planet Maridun. After they landed, Secura and Tano took Bly and the remaining troopers (except for Rex, who guarded Anakin during the night) to look for help. They found a drawing of a tree, so they looked for it, but some giant pods fell down, . Secura noticed that other pods had been dragged away by. Secura guessed that whatever or whoever had dragged away the pods were sentient creatures and thought they might be able to help Anakin. The group followed the tracks and were attacked by a pair of mastiff phalones and only Bly, Tano and Secura came out alive. The next morning, they found a village of Lurmen who had settled on the planet, far away from the war. The village elder, Tee Watt Kaa refused to aid them, fearing that destruction would break the peace they already had. However, at Tano's request, he did give them medical supplies and had his son, Wag Too help deliver them. But he requested that only one Jedi take the supplies and that Bly should follow. The Jedi agreed to this, Tano and Bly went to bring back Anakin, and the injured Jedi was healed.
Later, an army of droids, led by General Lok Durd, landed on Maridun and upon meeting Tee Watt Kaa, claimed the planet for the Separatists. The Jedi and the clones decided to leave the village, or else the droids would have killed the Lurmen. They left, but decided to steal a Separatist ship to get off of Maridun. They were followed by a spy droid, but they destroyed it before it could send news of their plans to the Separatists. The team climbed a tree and saw a Separatist fort and Durd testing a new weapon that destroyed life forms, but not machines. After the successful test, the Separatist army headed for the Lurmen village. The Jedi and the clones mounted a raid on the fort that night and stole a ship and two shield generators. They then headed back to the village. They offered their help, which Tee Watt Kaa turned down, but they then barricaded the village anyway. The Separatists reached the village and tried using their new weapon, but the shield generators stopped the effects of it. They then sent the droids out. Secura and the others obliterated the first wave, but the second group got past them and destroyed the shield generators. Secura and Tano took care of them while Skywalker destroyed the new weapon. After the battle, Wag Too thanked the Jedi for saving the village, and Kaa admitted that the Lurmen owe the Jedi their lives. Finally, three Jedi cruisers appeared and picked up Secura, Tano, Skywalker, Rex, and Bly.
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