Episode 3 is set another 4-5 years later. Anakin is now a Jedi Knight and fully involved in the war, specifically on any piloting missions. Obi Wan, now a general, is more involved with negotiations between systems and bring them to peace or onto the Republic’s side, trying to find a way to end the war. He is also in charge of investigating Maul and Dooku’s activities. Not too long into the movie Obi Wan and Anakin are reunited as Palpatine is kidnapped by Maul and Grievous. They get along like brothers and the two discuss how fragile Anakin’s ego must be multiple times. Obi Wan knows about Padme, and the twins. In a brief moment of seriousness Anakin tells Obi Wan to give Luke his lightsabre if anything should happen to him. Anakin asks Obi Wan to look after his family, especially Luke. Anakin sees Obi Wan as a father and brother, and wants Obi Wan to be the same for Luke.
After the defeat of Dooku and rescuing Palpatine, a series of events is set in motion. The third film stays somewhat the same, but instead of Obi Wan confronting Grievous he confronts Maul for the last time. Palpatine manipulates Anakin into believing he is the last good jedi. Mace Windu and a handful of Jedi realise Palpatine is the real Sith Lord and rally to kill him, however with Anakin’s help, Palpatine lives. Grievous is used by Palpatine after Anakin begins turning to the dark side to lure Anakin to Mustafar. His journey to the dark side almost complete. Anakin and Grievous fight, as instructed by Palpatine, and Anakin wins, killing Grievous as revenge for all his fallen friends.
Instead of it being Order 66, Palpatine informs the clones of Mace Windu and “his Jedi” attempting to assassinate him, to take over his position. Palpatine further manipulates the clones into believing the Jedi have been using clone troops as puppets and fodder in the war to take over the galaxy. The clones believe him and turn on their old Jedi allies. Palpatine uses the clones rage against the Jedi to complete his take over of the galaxy, winning the “Clone War”, bringing many star systems to his side. He has secured himself as Emperor of what he has chosen to call “The First Galactic Empire”.
Padme’s role and the birth of the twins changes significantly. Instead of being passive, she actively argues with Anakin on Palpatine, and is a voice against Palpatine in the Senate. She also doesn’t die in child birth. In fact, the twins are around 2 years old during the events of Revenge of the Sith, however the twins don’t see much of their father, and often see Padme worried. After the take over of the Empire, and purge at the Jedi Temple, Palpatine informs Anakin of his family’s deaths at the hands of the Jedi, a lie of course. In actual fact, Padme was the only one who died, trying to save Jedi from the clones attacks. Obi wan arrives in time to save Luke and Leia, and holds Padme until she dies in his arms. The children’s deaths are faked by Obi Wan and Yoda to protect them from The Emperor. They are taken by Obi Wan, to a safe place.
Later Obi Wan would fight Anakin/ Vader, and Yoda would fight Palpatine, in one last effort to save the Republic and Jedi Order. Yoda and Palpatine’s battle is mainly with the force and some lightabre combat. However, with a sneak move, Palpatine wins. Obi Wan and Vader’s have a lightsabre duel, using the force occasionally. Obi Wan tries to tell Anakin the truth, but Vader won’t listen to any more “Jedi lies” and immediately attacks. Obi Wan cuts off the robotic arm holding Anakin’s lightsabre and stabs him in the chest. He walks away, believing Vadar, and his old friend, had died from that fatal blow. As Obi Wan turns back he sees Anakin’s body has been set on fire and burns. He escapes before Palpatine finds sees him. Palpatine saves Vader, and we see most of Anakin is replaced by the machine we know as Darth Vader.
Yoda and Obi Wan discuss splitting the twins and going their separate ways. The movie ends in a similar fashion, Leia goes with Bail Organa and Luke goes to Owen and Beru to be raised on Tatooine. Obi Wan tells them that Anakin was killed by Darth Vader, and cautions them to not trust the Galactic Empire. Owen holds Obi Wan responsible for his best friends death. Obi Wan doesn’t have the heart to tell him the truth. Obi Wan leaves and looks back at the twin suns, he pulls his robes up over himself and we briefly see 3 lightsabres; his, Anakin’s, and Qui Gon’s.