The Separatist forces tracked Obi-Wan Kenobi, Siri Tachi, Anakin Skywalker, and Padmé Amidala by means of a tracer device planted in a foolproof codebreaker. This had been brought by Talesan Fry, who agreed to turn the codebreaker over to the Old Republic at a hidden base on Azure.
The base had meager defenses, and was badly outnumbered by the huge Separatist fleet. The Republic forces had to surrender control of the planet. General Solomahal, the general of the base, was determined not to let the codebreaker into Separatist hands, and before he was captured, he managed to destroy it.
As the Republic forces discovered the Separatists were planning to launch their attack on the weak planet of Azure, the Jedi took to their starfighters in an attempt to hold off the droids until clone reinforcements could arrive. Padmé was sent with Taly in a starship away from the battle—the Jedi hoped they would make it to hyperspace in time to avoid the conflict. Meanwhile, Anakin led the most skilled of the General Solomahal's space pilots into battle against the massive force of Tri-Droids. When the enemy began to fire on civilian ships, Padmé's was peppered with fire, and crashed, though two escape pods were launched. Siri and Kenobi peeled off from the main fight and worked their way to where the pods' had landed.
As the Jedi realized that the battle would be lost due to the droids' superior numbers, they contacted Solomahal. They told him to send the codebreaker away, and to prepare for evacuation. Refusing the suggestion, the General continued the fight, guarding the codebreaker himself. The Jedi arrived at the landing platform, but were soon surprised by Magus in his red-black starfighter, who immediately opened fire. Fleeing from his attack, they raced aboard ARC-170 starfighters, Padmé with Siri, and Taly with Obi-Wan.
On the other side of the battle, Anakin began to realize that though their casualties were low and the they had been doing well, they could not prevail against such a large army. After receiving a comm that Padmé's ship went down, he raced to the platform, hoping to save her if she had survived. As the Jedi and others fought against Magus, Siri concocted a risky plan. Crawling out of her ship and leaving Padmé in control, she leaped into the air and used the Force to land on Magus' ship, where she used her lightsaber to cut through the canopy. Magus began to fly wildly, jerking around, which forced Kenobi to launch a low-powered concussion missile in an attempt to stop him. The missile collided with the ship, knocking Siri into the cockpit and crashing the starfighter to the ground.
Magus was ejected from the ship, defeated. Obi-Wan jumped into the smoking ship to find Siri. He discovered that she had been shot by Magus, and barely alive. With her last breath, she gave Obi-Wan her warming crystal and confessed her love for him once more. Obi-Wan then began to allow his anger to overcome him, and came close to murdering Magus, but reigned in his emotions. He arrested Magus as a prisoner of war.
The droids bombed Taly's office and labs, destroying all of his inventions and work, most of which would be impossible to reproduce. Still fighting for a losing side, Solomahal was captured, though he destroyed the codebreaker shortly before his capture, stopping any chance of the Separatists obtaining it and its power. He later broke free and was given another command. Back at the Jedi Temple, Obi-Wan mourned Siri and walked through the halls, unable to sleep just like his master twenty years before when Qui-Gon Jinn lost Tahl. But in his pain, he finally understood what Qui-Gon had tried to teach him so long ago-that he could survive with the loss of the person he loved most. Obi-Wan had finally learned how to love with an open heart.
- Secrets of the Jedi (First appearance)