After sleeping with Mace Windu in order to "complete" her Jedi trials, she could usually be found wandering around the Jedi Temple, looking pretty and vacant. In fact, she was there the day Mace Windu ran around gathering as many Jedi as he could to mount a rescue operation of Obi-Wan Kenobi on Geonosis. Aayla survived the Battle that followed, and went on to fight in several battles throughout the Clone Wars.
On Felucia, she was killed by her own Clonetroopers, the 327th Star Corps, before Order 66 was even given. Commander Bly had finally had enough of her stupid banter and idiotic questions that he gave the order for his troops to open fire until there was nothing left of her. It was only after the blasterbolts ceased that Bly realized he had a voicemail from Chancellor Palpatine giving the order to kill all Jedi.
She won Miss Jedi Temple only once, which was a little surprising until you had a conversation with her. She was beaten by both Barriss Offee and Shaak Ti, especially when the two paired up for a colorful demonstration. Aayla dominated the final year of the pageant by dressing like a whore.