For two thousand years the Jedi enjoyed relative peace throughout the galaxy. They seemed to have had established methodologies and techniques that allowed their order to grow to over 10,000 members, allowing them influence in every corner of the galaxy. Their ancient enemies the Sith were extinct and had faded into memory and legend. Tales of the Sith were now used as ghost stories to scare youngling Jedi into behaving. The Jedi had waged their battles against the Sith and emerged victorious with the Sith utterly destroyed. Or so the Jedi thought.
When the Jedi defeated the Sith for the final time two thousand years prior, a sole survivor changed the dynamics of the Sith order forever, and set in motion plans to bring down the Jedi order and exact revenge no matter how long it took. For two thousand years the Sith worked from the shadows hidden from the galaxy as well as the Jedi. Perhaps the greatest trick the Sith ever pulled was convincing the Jedi they did not exist. Finally, the opportunity presented itself and the Sith made their move at the height of the Clone Wars to all but annihilate the Jedi.
During the Clone Wars, the Jedi were faced with a difficult dilemma. The Jedi were keepers of the peace, dedicated to upholding justice. However, this new war called into question the role of the Jedi. Tradition mandated that the Jedi held no alliances to any one government, but tradition over the past millennia informally allied the Jedi with the Old Republic. Now that Republic was asking the Jedi to lead troops into battle in its defense, to defend a government many Jedi believed had grown corrupt and ineffective.
These questions and doubts fractured the Jedi from within and war swept through the galaxy so quickly, there was little time to contemplate these issues. All the Jedi could do was what they thought best while trying to hold their crumbling order together. In the end, the Jedi Order was virtually destroyed. Those that weren't killed during the war were hunted down and exterminated. However, like the Sith before them, a small part of the Jedi Order managed to survive and would eventually return to face their enemy.