Episode 2 would begin four years after the events in episode 1. Anakin is being trained during the clone wars, and often hears about how his fellow padawans and friends are being killed. Despite the wisdom of both Obi Wan and the council, rage and anger build inside of him. He also hears about how his friends, Owen and Beru, have been captured by the Separatists. Anakin goes to free his friends, but falls prey to the trap of the darkside as he gives in to the anger he’s been building. We would also see how Palpatine has been acting as a mentor to him, and how his beliefs are conflicting with Obi Wan’s training.
Obi Wan is somewhat involved as a general in the war, but his main effort is in the ongoing investigation he started in Episode 1, whilst training a headstrong Anakin. The trail has gone cold for almost 2 years when suddenly he is contacted by Qui Gon’s master, Count Dooku, who disappeared to the unknown regions shortly after Obi Wan became Qui Gon’s padawan.
There is a belief amongst the Jedi and people of the Republic, that Maul was a Sith apprentice, and the master is a Sith Lord, organising the Separatist’s current movements. Palpatine has been able to get a lot of power during this time, as elected by the people of the Republic. Queen Amidala has ended her term, and makes arrangements to see Anakin. The spark is quickly rekindled as Anakin is tasked with protecting her after Jango Fett makes a move to kill her. The two eventually end up married by the end of the film.
Episode 2 would reveal that Maul is alive and working with Dooku, confirming the belief and giving credibility to Palpatine, who has been backing this theory since the beginning of the war. More and more Jedi believe this theory, with only Obi Wan, Yoda, and a few more suspicious. This plays out into the next movie. The second film shows how caught up the Jedi have gotten in the war, the Jango Fett conspiracy, a trap, setup by Dooku, that the Jedi fall into in which a lot of them die, culminating at the battle of Geonosis. The more the jedi try to untangle certain events, the more confused they become, showing how clever Palpatine has been the entire time.