After the battle of Naboo, Qui-Gon Jinn went on a galactic walkabout. He traveled to many lost Jedi worlds seeking answers. Eventually he found his way to Tython, a planet in the deep core that was the birthplace of both the Jedi and the Sith. He discovered there that the planet and it’s moons were so attuned to the force, that shifts both towards the light and dark sides of the force would cause chaotic storms, and earthquakes.

He then understood what the Jedi of millennia past had forgotten. That the force could never be in balance if force users only walked in light or in darkness. Every force user must walk that third path.

And so, The Order of the Third Path was founded there on Tython. 

over the decades Qui-Gon trained many Third Path disciples, but in his old age he became more and more militant about his beliefs.

Eventually, he came to the decision that to preserve the safety of the galaxy, both the Jedi and the Sith must be destroyed. So him and his Third Path Zealots, came out of hiding and began their attacks