Amidala was then sent on a mission by Palpatine to negotiate with a representative of the Banking Clan about withdrawing from the war. She, along with C-3PO, traveled to the rendezvous. However, Amidala learned that it was all a trap when she came out in the middle of a battle between the Republic fleet and the Confederacy's heavy cruiser, the Malevolence. She tried to move away from the heavy cruiser, but was pulled in by the Malevolence's tractor beam. Though she urged the Republic fleet to continue their attack, refusing to allow herself to become a bargaining chip, her husband ordered them to stop. As her ship set down in the hangar bay, Amidala rigged it to blow in the hopes that it might take Grievous with it. The ship did indeed explode with the general aboard, taking several battle droids with it, but he survived. She and C-3PO then escaped from General Grievous into the bowels of the Malevolence. She was able to contact Skywalker and Kenobi, who had boarded the ship to rescue her.

The two groups met at a point halfway between them, though Skywalker and Amidala soon became separated from Kenobi, Threepio, and Artoo. While Kenobi was forced to delegate the rescue of 3PO to R2, to ensure that the hyperdrive stayed offline, Skywalker and Amidala made their way to the bridge to make adjustments to the navicomputer that would cause the Malevolence to fly into a moon. Both missions proved a success, and the group managed to escape the Malevolence.

While Grievous personally took his starfighter, the Soulless One, and several other fighters that attacked the group as they attempted to dock with the Republic fleet, the Malevolence began to move towards a near moon, before colliding with it, destroying the heavy cruiser instantly. With the loss of the Malevolence, Grievous fled the battle, and Amidala and her companions reached safety.