A more subtle conflict took place when Separatist agents kidnapped Jabba the Hutt's nephew Rotta. Believing that the Republic was behind the crime, Jabba threatened to cut off access to the Hutt hyperspace lanes. Anakin Skywalker and Ahsoka Tano rescued Rotta, and exposed Count Dooku as the guilty party. Palpatine expressed his gratitude to the two Jedi for their help, and the Republic remained on good terms with the Hutt cartels.

As the war progressed, Chancellor Palpatine took every opportunity to assist Anakin Skywalker. He recognized that Anakin's skill with the Force would make him a powerful Sith apprentice, and Palpatine assumed a role as Anakin's mentor and father figure.

On Malastare, fighting between the Republic and the Separatists accidentally awakened the legendary Zillo Beast. Palpatine gave his approval to Anakin Skywalker's suggestion that they knock out the creature and transport it offworld, believing that Republic scientist Sionver Boll could learn new biological secrets by examining the Zillo Beast in a laboratory on Coruscant.

The Zillo Beast escaped from its captivity after Palpatine ordered its death. The beast struck back by seizing Palpatine's shuttle in its claw, trapping the chancellor along with Padmé, Anakin, and the droids R2-D2 and C-3PO. Palpatine escaped certain death thanks to R2-D2's rocket jets, and the Zillo Beast perished when struck with toxin bombs. In the aftermath, Palpatine ordered Dr. Sionver Boll to secretly clone the dead animal for scientific study.

On Mandalore, the Death Watch threatened the population and Palpatine saw an opportunity for the Republic to take an active role. He introduced a doctored holorecording before the Senate that urged for immediate Republic intervention on Mandalore to stop the Death Watch. Duchess Satine Kryze of Mandalore, realizing that the recording had been faked, worked with Padmé Amidala to uncover the untampered original. The Senate cancelled the invasion in a public embarrassment for Palpatine.

When Cad Bane made a bold strike on the Senate building, he seized a group of senators and demanded that Palpatine release Ziro the Hutt from prison in exchange for the lives of his hostages. Palpatine gave in to the bounty hunter's demands.

Near the end of the war, Darth Sidious arranged for General Grievous to launch a massive assault on the capital, using the chaos as cover so Grievous could land on the surface and capture Chancellor Palpatine as a prisoner of war. Palpatine waited for rescue aboard Grievous' flagship. Before long, Anakin Skywalker and Obi-Wan Kenobi penetrated the Separatist starfighter screen and landed aboard the flagship, fighting their way to Palpatine's location.

When Count Dooku intercepted them, he lost both of his hands in Anakin's furious counterattack. Now utterly at Anakin's mercy, Dooku listened helplessly as Palpatine urged the young Jedi to take his enemy's life. Anakin did as the chancellor asked, beheading his beaten foe and taking another step toward the dark side of the Force.

After freeing Palpatine, Anakin and Obi-Wan tried to escape the damaged dreadnought as General Grievous tried to cut them off. But the Republic warships above Coruscant had inflicted severe damage on the flagship, and Grievous decided to flee in an escape pod. The stricken dreadnought slowly slid into Coruscant's atmosphere. Anakin somehow steered the vessel into a miraculous crash landing on the surface.

Once he had recovered from the adventure, Palpatine took in a performance at the Coruscant opera house with Anakin as his guest. Palpatine spoke about the war's progress and of Anakin's recent appointment to the Jedi Council, which had been pushed through at the chancellor's request. Anakin had been suffering from nightmares about losing his love Padmé, and took interest as Palpatine related a story about his Sith Master Darth Plagueis.

Palpatine carefully framed the tale as an "old Sith legend," but the revelation that dark powers could prevent the death of a loved one opened Anakin's mind to the possibility that he might need to disobey the Jedi Order and pursue forbidden knowledge to save those he cared about.

Later, Anakin visited the chancellor in his offices and the truth came out. Palpatine admitted that he possessed the power of the dark side, and Anakin realized that the chancellor was the sinister mastermind the Jedi had been hunting since before the start of the Clone Wars. Stunned by the revelation, Anakin returned to the Jedi Temple to inform Mace Windu.

Master Windu ordered Anakin to remain behind in the Temple, while he and a hand-picked team set out to apprehend the chancellor for his crimes. Mace Windu arrived in Palpatine's offices and announced his arrest. Palpatine scoffed at the news that the Senate would determine his fate, and with a roar of "I am the Senate," he ignited a red-bladed lightsaber.

Before the Jedi could react, Palpatine sprang into action and killed all of them except Mace Windu. Anakin, tormented by the thought that the ability to save Padmé might be lost with Palpatine, traveled to the chancellor's office and burst in as Mace Windu pointed his lightsaber at Palpatine's heart.

Palpatine fired Force lightning in defense, but Windu used his lightsaber blade to reflect it back on its wielder. The energy crawled over Palpatine's face, leaving it a melted, sunken mask. Knowing that Windu would kill Palpatine, Anakin interfered and severed Windu's hand. Palpatine took action, unleashing a barrage of lightning that blasted Windu through a window to his death.

Palpatine went before the Senate to deliver an emergency address. With his disfigured face hidden in the shadows of a hood, Palpatine claimed to have survived a Jedi assassination attempt. He denounced the conspiracy of the Jedi, and delivered the good news that victory in the Clone Wars had at last been achieved. Palpatine declared that he was marking the triumph by inaugurating the first Galactic Empire, with himself as its leader.

The Senate responded with cheers, its members taken in by Palpatine's play for sympathy and grateful to the chancellor for winning the war. Senators Bail Organa and Padmé Amidala looked on, with Padmé remarking, "This is how democracy dies. With thunderous applause." Now possessing ultimate power, Palpatine had no further need to cultivate two identities. Despite his public title of Emperor Palpatine, he was Darth Sidious in thought and action from this point forward.