The Great Jedi Purge

The Purge begins shortly before the end of the Clone Wars, which had been conceived as part of a scheme by Chancellor Palpatine to eliminate the Jedi and establish himself as the Emperor of the Star Wars galaxy.

At some point between the known events of Episodes II and III, members of the Jedi council began to suspect Chancellor Palpatine was tied to Sidious and Count Dooku's Separatist army. In Revenge of the Sith, Jedi Master Mace Windu openly states to the Jedi Council that he no longer trusts the Chancellor; Obi-Wan Kenobi expresses similar misgivings.

Anakin Skywalker, then believed to be the "Chosen One" of Jedi prophecy, finds out that Palpatine is actually Darth Sidious, the Dark Lord of the Sith for which the Jedi have been searching for more than a decade. Anakin reveals this information to Windu, who then leads a small team of fellow Jedi Masters - Agen Kolar, Saesee Tiin and Kit Fisto - to apprehend Sidious. In the ensuing lightsaber duel, Sidious quickly and effortlessly kills all but Windu, who defeats him. As Windu reasserts Palpatine's arrest, however, Anakin suddenly enters the room while Palpatine is apparently pleading for his own life. Palpatine had long been nurturing the young Jedi's desire for power and had recently roused Anakin's fear for the safety of his pregnant wife, Padmé Amidala. Before Windu can strike down the Chancellor after fending off a sneak attack by the Sith, Anakin severs Windu's hand with his lightsaber. Sidious then springs to life and blasts Windu with a torrent of Force lightning, which throws him out the window to his apparent death. Agen Kolar, being the first to die at the hands of Darth Sidious is effectively the first victim of the Great Jedi Purge, followed within moments by Tiin and then Fisto.

Anakin thought he was doing the right thing saving Palpatine’s life when he cut off Windu's hand with his lightsaber. However, Anakin did not think that Palpatine would kill Windu, and as a result of Windu's death Anakin believed that he had gone too far to be forgiven. To save his life, he had no other choice but to join with Palpatine.