The Jedi have been removed from office.  No longer trusted by the populace to use their powers for good, most Jedi have gone into hiding.  The rest still work for the Republic as glorified slaves, not trusted to make decisions on how best to use their power.

With the public trust in the Jedi Order obliterated and their abilities suppressed, enemies of the Republic are nipping at the edges.  The Sii-ruuvi are poised to invade if the Republic shows weakness.  The Yuuzhan-Vong are offering to buy Jedi slaves.  Dathomir has left the Republic and is a haven for the Jedi who trust the witches.

Will the Republic fall without the Jedi or will it realize that it needs the Jedi even more than the Jedi need the Republic?

Star Wars: Darkness from Within