After the Battle of Naboo and the capture of Darth Maul, The Jedi Council was forced to accept that a war was coming. Because of that, they began focusing their training more and more on martial talents, rather than focusing on diplomacy as they had since the disappearance of the Sith.
Anakin Skywalker excelled at the Temple. His growing prowess at combat impressed all his teachers, and even the most conservative masters who were wary of the Order's new direction praised his skill. He was the poster-boy for the new breed of Jedi: Soldiers first, peace-keepers second.
Jedi Master Sifo-Dias, The Council-Member who was one of the loudest proponents of Jedi Militarization considered taking him on as a Padawan, before he was killed by his rival and then-fellow Jedi master Dooku.
Dooku had been one of the loudest detractors of militarization, and after his murder of a fellow Jedi master and subsequent dissapearance, any talk of returning the order to a peace-keeping organization fell on deaf ears.
(Dooku had also been in favor of the jedi distancing themselves from the republic, and relocating their temple off Coruscant. Many Jedi agreed with his distrust in the republic, a sentiment that would become more common once the Clone Wars began. I'll have many more details of the internal politics of the Jedi in a later write-up)
After Master Sifo-Dyas's death, Skywalker was taken as a Padawan Learner by the now-Master Obi-Wan Kenobi. Between missions, he also began taking private saber combat lessons from the Battlemaster of the Jedi Order: Mace Windu. Under Windu's tutalage, he mastered every saber form except for Vaapad, a style Windu insisted he wasn't ready for, and also trained in dual saber and double-bladed saber combat. Mace Windu intended for Skywalker to eventually succeed him as Battlemaster of the Order.
One year prior to the Battle of Geonosis, Anakin Skywalker passed the Trials and became the youngest Jedi to attain the rank of Knight in over a century. Many Jedi considered this a mistake, and believed him unworthy of the title.
(it should be noted that most events in Attack of the Clones play out differently. Shmi is still a slave, and is still alive. Anakin never went back to Tatooine to save her. Never went all Adam Lanza on those Tuskens, and doesn't lose his hand fighting Dooku)
THE CLONE WARS ERA BEGINS Edit
A few months after the Battle of Geonosis, Anakin started feeling troubled by the fact that he had never kept his promise to his mother to return to Tatooine to free all the slaves. So he goes to the Council to beg them to allow him to go on a mission to Tatooine to do just that. They are unanimous in their refusal.
Moments after leaving the Council Chambers, Anakin is contacted by Chancellor Palpatine, who offers him Command of the 501st Legion of Clone Troopers to go to Tatooine to free the slaves and build a Republic-Controlled base. Anakin agrees.
The Jedi Council quickly realized that they were being spied on for the chancellor, and trust in the Republic hit an all-time-low.
Jedi began refusing to work with clone troopers, and began recruiting and training Militias loyal to the Jedi. Many of these soldiers were former Jedi Younglings who had failed to become Padawans and were working on Tanaab, Bandomeer, and other AgriCorps worlds.
The Council sent Kenobi to Tatooine to convince Anakin to return to the temple without completing his mission. Anakin attacks his former master in anger, convinced that he had betrayed him. Kenobi cuts off Anakin's right arm.
Anakin Skywalker is expelled from the Jedi Order.
Looking for an outlet for his rage at being betrayed by the man he saw as a father, He asked Chanceller Palpatine to instate him as a General in the Grand Army of the Republic. Palpatine agreed, and put him back in command of the 501st.
He began thinking of his time as a Jedi as comparable to when he was a slave. To him, the name "Anakin Skywalker" was the name of a slave and nothing more, so he disposed of it and took the name "Vader"
Over the years, many Jedi began to see that winning a war and following the Jedi code were mutually-exclusive, and followed General Vader's example. Nearly half of the Jedi order left the order to fight the separatists without having to answer to the Jedi Council.
The Jedi Order became more and more distrustful of the Republic, and began withdrawing from the war completely. This made the average citizen, along with most of the government resent the Jedi. It also meant that very few people questioned Order 66.
THE JEDI CRUSADES ERA BEGINS Edit
Not long after Order 66, Padme ran away and gave birth to Luke and Leia Skywalker on Tatooine. The Still-General Vader tracks her down and kills her, but not before Kenobi escapes with the twins.
Following misinformation spread by the Jedi, Vader goes to Mustafar believing that is where the Jedi are keeping his children. Instead it is a trap. Mace Windu is waiting for him, and after an extremely long duel, Windu is victorious. Vader is cut in half at the waist, and left to die by his former teacher. Palpatine arrives to save Vaders live.
Palpatine then takes Vader as his Sith apprentice, and General Vader becomes Darth Vader.