In the morning, Anakin told Padmé that he had a nightmare about his Mother, Shimi Skywalker was dying, and asked her to accompany him to Tatooine since he wouldn't be disobeying the Jedi Council or his master orders with her with him. While on Tatooine, the two found out that from Waldo that Shimi Skywalker was freed and married by a moister farmer named
Cliegg Lars. When arriving at the Lars farm, they were greeted by C-3PO,
Owen Lars and Cliegg Lars. Cliegg informed Anakin that her mother was kidnapped by Tusken Raiders. Anakin refused to believe that she was dead, and went to search for him leaving Padmé with the Lars. The next morning, Anakin returned with the lifeless body of his mother. Deeply disturbed by her death, Anakin confessed to Padmé that he killed the the Tusken Raiders that took her mother captive. Padmé attempted to comfort him for his loss.

Battling droids and looking sexy
During the funeral of Anakin's mother, R2-D2 arrived with a message from Obi-Wan to transmit his message to Coruscant about his discovery on the planet Geonosis. It was revealed that Count Dooku and Nute Gunray were behind the assassination attempt on Senator Amidala and that he joined the Separatist movement. The message ended with Kenobi being captured by the Separatist. While Jedi Master
Mace Windu told Anakin to stay and protect Amidala while the Jedi rescue Obi-Wan, however, Padmé was able to convince Anakin to come with her to
Geonosis by twisting Windu's words. Joined by C-3PO, they headed for Geonosis. After arriving on Geonosis, both Padmé and Anakin was captured and were sentenced to execution. Before being brought to the execution arena, Padmé, believing that they were going to die, confessed to Anakin that she loved him and shared a kiss. The two were then chained on three stone pillars with Obi-wan waiting for them. Before being chained however, Amidala was able to hide a pick to unlock the chains for herself when the time was right. The trio did all they could to delay their death. Amidala was slashed across the back by the nexu creature but managed to hold him until Anakin came to rescue her. After a small struggle, Mace Windu and a Jedi strike team arrived to help. After a long battle against battle droids, the Jedi started to become overwhelmed by the number of battle droids and begin to make their final stand when Master
Yoda arrived with Clone troopers to rescue them. In order to stop the war from escalating even further, Amidala joined Skywalker and Kenobi to stop Count Dooku from leaving the planet, but got separated from them when she fell out of the clone ship. After getting another squad of clone troopers, Amidala arrived to hanger just after Dooku took off.
After the Battle of Geonosis, Padmé and Anakin got married secretly on Naboo with C-3PO and R2-D2 as the only witnesses.

Padme during the Clone Wars
In Star Wars: The Clone Wars, Padmé learns of Anakin and his padawan
Ahsoka Tano's mission in rescuing
Jabba the Hutt's son,
Rotta after being "kidnapped" by the Separatist. On Coruscant, Amidala goes to search for Jabba's uncle, Ziro the Hutt to see if he could be of help to find Rotta, but he refused. Amidala then found out the Ziro was in league with Count Dooku so that he could receive full control of the Hutt clan from his nephew. Before she could manage to tell anyone about his plot, Padmé was caught. However while captured, Amidala managed to trick the guard droid into turning on its comlink so she could call C-3PO for help. C-3PO arrived just in time with guards before Padmé was about to be killed. She then managed to contact Jabba just in time to save both Anakin and Ahsoka before Jabba could kill them, telling him that it was Ziro who betrayed him. Afterward, Amidala helped work out an alliance between the Republic and Hutts for the Clone troopers to access Hutt hyperspace routes to help give the advantage for the Republic against the Separatist.
In
Star Wars Episode III: Revenge of the Sith, three years have past since the start of the Clone Wars. After rescuing Supreme Chancellor Palpatine from Count Dooku, Anakin Skywalker reunited with Padmé Amidala in the shadows. From there, Amidala revealed to him that she was pregnant. At first she was fearful that the Jedi Council might find out, but Anakin reassured her that this baby was a blessing and that everything would be fine.
The two spent the night at Amidala's apartment however, during the night, Anakin had a nightmare about Amidala and the baby. Padmé managed to get Skywalker to tell her what he saw in his nightmare and that it was that she died after childbirth, but couldn't see what happened to the baby. The next day, Amidala found out that Palpatine made Skywalker the representative for the Jedi Council, and asked him to persuade Palpatine in giving back the emergency powers back to the senate, but he refused.

Where have you been? Oh you know, killing younglings
Later that night, Padmé could only watch in fear, worrying for Skywalker's safety, as she saw smoke coming from the Jedi Temple as an armada of Clone Troopers attacked. Little did she know, it was Anakin, now Darth Vader, who was leading the attack. In the morning, Amidala was relieved to find out that Anakin was alive. He told her that Palpatine is sending him to the planet
Mustafar to meet with the Separatist and end the war. Later, Amidala attended a special hearing in the senate by Palpatine. Palpatine convince the senate that the Jedi was plotting against the Republic, and decided that from this day forth, the Republic would transform into the Galactic Empire. She could only watch as the Republic and liberty die in the senate. After the announcement by Palpatine, Padmé was visited by Obi-Wan Kenobi who told her that Palpatine was the Sith lord the Jedi was looking for, Anakin has turned to the Dark side and where he could be. Amidala refused to believe that Anakin has turned to the Dark side and refused to tell Kenobi where he could be, in fear that he would kill him. When Kenobi left, Padmé decided to find out for herself if Anakin did turned and with C-3PO, she headed for Mustafar. Little did she know, Kenobi sunk aboard her starship.
When she arrived at Mustafar, Padmé confronted Anakin (Vader) about what she learned from Obi-Wan and found out that it was true. Amidala tearfully pleaded to Anakin to stop what he was doing and come back to the light, however, when Kenobi revealed himself from Amidala's starship, Anakin was convinced that Padmé betrayed him so that Kenobi could kill him, and began to Force choke her. Kenobi managed to draw Anakin's attention towards him and he released his hold on her. C-3P0 and R2-D2 managed to get her aboard her starship.
After Kenobi defeated Vader, he took Amidala to Polis Massa where Master Yoda and Senator
Bail Organa awaited as well, for medical attention. It was from there that the medical droids told them that Amidala was dying because she lost the will to live. Before she passed away, she gave birth to not only one, but two twin babies:
Luke and
Leia Amidala Skywalker. In her final moments, she told Obi-Wan that she still believed that Anakin had some good left in him. She passed away afteward.
In the aftermath, Padmé was buried back on Naboo and her two children, Luke and Leia, were seperated: Luke went to live with his step-uncle Owen Lars and his now wife,
Beru on Tatooine while Obi wan watched from afar, while Leia was adopted by Amidala's closest friend and ally, Senator Bail Organa and his wife.