Ten years after the Invasion of Naboo, former Jedi Count Dooku became the public face of a Confederacy of Independent Systems that had withdrawn from the Republic in opposition to the corruption they believed had enveloped the Senate. In response to the threat posed by this Separatist Alliance, the Republic Senate debated the proposed Military Creation Act that would allow Supreme Chancellor Palpatine to formally commission a Grand Army of the Republic. During this time, Amidala became a member of the Chancellor's Loyalist Committee and was regarded as the leader of the opposition to the Military Creation Act.

Loyalist Committee-AOC
Amidala and the Loyalist Committee meet with Chancellor Palpatine.
On the eve of the vote in the Senate over the Military Creation Act, Amidala arrived on Coruscant. Upon landing, her cruiser was hit in an assassination attempt by bounty hunter Zam Wesell, who had been hired to kill Amidala by Jango Fett, himself under the employee of Count Dooku. The explosion killed several of her guards as well as Amidala's double, Cordé. At the request of Supreme Chancellor Palpatine, the Jedi Council assigned Jedi Knights Obi-Wan Kenobi and Anakin Skywalker to protect Amidala and investigate the incident, though Amidala objected to the added security. That evening, Amidala met with Kenobi and Skywalker in her penthouse apartment. With several years having passed, Skywalker was nervous to meet Amidala and while she hid her feelings, Kenobi noted that the senator was pleased to see Skywalker as well. That night, Zam Wesell tried again to kill Amidala by releasing two deadly kouhuns into her apartment using a droid. Kenobi and Skywalker sensed the attack and rushed into the bedroom. Skywalker managed to kill the kouhuns, and Kenobi jumped through the bedroom window and grabbed on to the droid as security officers rushed into the apartment. Kenobi and Skywalker, after a chase through the Coruscant skylanes, were able to capture Zam Wesell. Before she could reveal the plot behind the assassination attempts on Amidala, Wesell was killed by Jango Fett using a Kamino dart.

In the aftermath of continued attacks, Amidala was convinced to leave Coruscant and to return to Naboo. While Skywalker went with her to continue protecting her, Kenobi continued the investigation into the assassination attempts. Upon arriving on Naboo, Amidala and Skywalker grew closer in their relationship, and Skywalker told her of his love for her. However, since Skywalker was committed to the Jedi Order and Amidala to the Senate, they both agreed to forgo pursing a more romantic relationship. While on Naboo, Skywalker started experiencing Force visions of his mother in danger. Convinced he had to save her, he determined to travel to Tatooine. Amidala traveled with him, and upon their arrival at the Lars moisture farm, Skywalker discovered that his mother had been taken by Tusken Raiders. He was able to track them down, but was too late, and his mother died in his arms. Angered, he slaughtered the entire village including the women and children. He returned to the homestead to bury his mother. Later, Skywalker confessed to Amidala his despair and anger and what he had done, and she attempted to comfort him.