There are many reasons why the Jedi lost in the Clone Wars and fell into the trap of the Sith, however none is as fundamental as this one: the Jedi lost as soon as the war started. Allow me to explain. Everything about war is fundamentally against what it means to follow the path of the Jedi. "Wars not make one great," as Yoda once said. In Shatterpoint, a novel that takes place relatively soon after the war started, Mace Windu finds out first hand from his former padawan, Depa, on how a Jedi would immediately have to abandon their Jedi principles to participate in the war.

Winners and losers alike end up killing, sometimes brutality, and often at the expense of civilians. In Medstar I and Mestar II, Bariss Offee learns that walking the path of the Jedi is like walking on the edge of a blade, and you can easily fall to the dark side. Furthermore, when you do fall to the darkside, you believe you are doing the right thing - blind by your range, anger, and hate. Anakin does exactly this in Jedi Trial when he taps into the dark side as he rescues thousands of his troops and captures the banking clan leader that had taken their strategic communicatoins center.

You may be asking why did the Jedi agree to lead the clone troopers? Well, I asked myself this as well. Presumably had the Jedi stayed true to their principles and refused to partake in war, they would have never lost to the Sith. In one of the dark horse Clone Wars Comics, we are told that they did try to refuse to lead the clones, but Palpatine insisted stating that there was no other organization that had the cunning, wits, and intelligence to command such a large army. Had there been another way, a way to try and bring peace without directly leading an army, maybe the Jedi could have stopped the war and discovered Palpatine .